@phdthesis{Ankenbrand2018,
  author    = {Ankenbrand, Markus Johannes},
  title     = {Squeezing more information out of biological data - development and application of bioinformatic tools for ecology, evolution and genomics},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-156344},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {New experimental methods have drastically accelerated the pace and quantity at which biological data is generated. High-throughput DNA sequencing is one of the pivotal new technologies. It offers a number of novel applications in various fields of biology, including ecology, evolution, and genomics. However, together with those opportunities many new challenges arise. Specialized algorithms and software are required to cope with the amount of data, often requiring substantial training in bioinformatic methods. Another way to make those data accessible to non-bioinformaticians is the development of programs with intuitive user interfaces. In my thesis I developed analyses and programs to tackle current problems with high-throughput data in biology. In the field of ecology this covers the establishment of the bioinformatic workflow for pollen DNA meta-barcoding. Furthermore, I developed an application that facilitates the analysis of ecological communities in the context of their traits. Information from multiple public databases have been aggregated and can now be mapped automatically to existing community tables for interactive inspection. In evolution the new data are used to reconstruct phylogenetic trees from multiple genes. I developed the tool bcgTree to automate this process for bacteria. Many plant genomes have been sequenced in current years. Sequencing reads of those projects also contain data from the chloroplasts. The tool chloroExtractor supports the targeted extraction and analysis of the chloroplast genome. To compare the structure of multiple genomes specialized software is required for calculation and visualization of the relationships. I developed AliTV to address this. In contrast to existing programs for this task it allows interactive adjustments of produced graphics. Thus, facilitating the discovery of biologically relevant information. Another application I developed helps to analyze transcriptomes even if no reference genome is present. This is achieved by aggregating the different pieces of information, like functional annotation and expression level, for each transcript in a web platform. Scientists can then search, filter, subset, and visualize the transcriptome. Together the methods and tools expedite insights into biological systems that were not possible before.},
  language  = {en}
}
@phdthesis{Gerlach2018,
  author    = {Gerlach, Jennifer},
  title     = {Influence of Myc-interacting proteins on transcription and development},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-154917},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {The transcription factor Myc interacts with several co-factors to regulate growth and proliferationand thereby enables normal animal development. Deregulation of Myc is associated witha wide range of human tumors. Myc binds to DNA together with its dimerization partner Max, preferentially to canonical E-box motifs, but this sequence-specific interaction is probably not sufficient for Myc's binding to target genes. In this work, the PAF1 complex was characterized as a novel co-factor of Myc in Drosophila melanogaster. All components of the complex are required for Myc's recruitment to chromatin, but the subunit Atu has the strongest effect on Myc's binding to target genes through ist direct physical interaction with Myc. Unexpectedly, the impact of Atu depletion on the Expression of Myc target genes was weak compared to its effect on Myc binding. However, the influence of Atu becomes more prominent in situations of elevated Myc levels in vivo . Mycrepressed as well as Myc-activated targets are affected, consistent with the notion that Myc recruitment is impaired. An independent set of analyses revealed that Myc retains substantial activity even in the complete absence of Max. The overexpression of Myc in Max0 mutants specifically blocks their pupariation without affecting their survival, which raised the possibility that Myc might affect ecdysone biosynthesis. This connection was studied in the second part of this Thesis which showed that Myc inhibits the expression of ecdysteroidogenic genes and thereby the production of ecdysone. Myc most likely affects the signaling pathways (PTTH and insulin signaling) upstream of the PG, the organ where ecdysone is produced. By combining existing ChIPseq, RNAseq and electronic annotation data, we identified five potential Maxindependent Myc targets and provided experimental data that they might be involved in Myc's effect on Max mutant animals. Together our data confirm that some Myc functions are Max-independent and they raise the possibility that this effect might play a role during replication.},
  subject      = {Taufliege},
  language  = {en}
}
@phdthesis{Narkhede2018,
  author    = {Narkhede, Yogesh},
  title     = {In silico structure-based optimisation of pyrrolidine carboxamides as Mycobacterium tuberculosis enoyl-ACP reductase inhibitors},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-152468},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {The high infection rates and recent emergence of extremely drug resistant forms of Mycobacterium tuberculosis pose a significant challenge for global health. The NADH- dependent enoyl-ACP-reductase InhA of the type II mycobacterial fatty acid biosynthesis pathway is a well-validated target for inhibiting mycobacterial growth. InhA has been shown to be inhibited by a variety of compound series. Prominent classes of InhA inhibitors from literature include diaryl ethers, pyrrolidine carboxamides and arylamides which can be subjected to further development. Despite the progress in this area, very few compounds are in clinical development phase. The present work involves a detailed computational investigation of the binding modes and structure-based optimisation of pyrrolidine carboxamides as InhA inhibitors. With substituents of widely varying bulkiness, the pyrrolidine carboxamide dataset presented a challenge for prediction of binding mode as well as affinity. Using advanced docking protocols and in-house developed pose selection procedures, the binding modes of 44 compounds were predicted. The poses from docking were used in short molecular dynamics (MD) simulations to ascertain the dominant binding conformations for the bulkier members of the series. Subsequently, an activity-based classification strategy could be developed to circumvent the affinity prediction problems observed with this dataset. The prominent motions of the bound ligand and the active site residues were then ascertained using Essential Dynamics (ED). The information from ED and literature was subsequently used to design a total of 20 compounds that were subjected to extensive in-silico evaluations. Finally, the molecular determinants of rapid-reversible binding of pyrrolidine carboxamides were investigated using long MD simulations.},
  subject      = {Tuberkelbakterium},
  language  = {en}
}
@phdthesis{Slawig2018,
  author    = {Slawig, Anne},
  title     = {Reconstruction methods for the frequency-modulated balanced steady-state free precession MRI-sequence},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-162871},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {This work considered the frequency-modulated balanced steady-state free precession (fm-bSSFP) sequence as a tool to provide banding free bSSFP MR images. The sequence was implemented and successfully applied to suppress bandings in various in vitro and in vivo examples. In combination with a radial trajectory it is a promising alternative for standard bSSFP applications. First, two specialized applications were shown to establish the benefits of the acquisition strategy in itself. In real time cardiac imaging, it was shown that the continuous shift in frequency causes a movement of the bandings across the FOV. Thus, no anatomical region is constantly impaired, and a suitable timeframe can be found to examine all important structures. Furthermore, a combination of images with different artifact positions, similar to phase-cycled acquisitions is possible. In this way, fast, banding-free imaging of the moving heart was realized. Second, acquisitions with long TR were shown. While standard bSSFP suffers from increasing incidence of bandings with higher TR values, the frequency-modulated approach provided banding free images, regardless of the TR. A huge disadvantage of fm-bSSFP, in combination with the radial trajectory, is the decrease in signal intensity. In this work a specialized reconstruction method, the multifrequency reconstruction for frequency-modulated bSSFP (Muffm), was established, which successfully compensated that phenomena. The application of Muffm to several anatomical sites, such as inner ear, legs and cardiac acquisitions, proofed the advantageous SNR of the reconstruction. Furthermore, fm-bSSFP was applied to the clinically highly relevant task of water-fat separation. Former approaches of a phase-sensitive separation procedure in combination with standard bSSFP showed promising results but failed in cases of high inhomogeneity or high field strengths where banding artifacts become a major issue. The novel approach of using the fm-bSSFP acquisition strategy with the separation approach provided robust, reliable images of high quality. Again, losses in signal intensity could be regained by Muffm, as both approaches are completely compatible. Opposed to conventional banding suppression techniques, like frequency-scouts or phase-cycling, all reconstruction methods established in this work rely on a single radial acquisition, with scan times similar to standard bSSFP scans. No prolonged measurement times occur and patient time in the scanner is kept as short as possible, improving patient comfort, susceptibility to motion or physiological noise and cost of one scan. All in all, the frequency-modulated acquisition in combination with specializes reconstruction methods, leads to a completely new quality of images with short acquisition times.},
  subject      = {Kernspintomografie},
  language  = {en}
}
@phdthesis{Weidner2018,
  author    = {Weidner, Magdalena Theodora},
  title     = {Brain serotonin throughout development - for better and for worse},
  publisher = {Magdalena T. Weidner},
  address   = {Maastricht, the Netherlands},
  isbn      = {978-94-6233-940-8},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-163345},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {The work presented in this thesis covers the effects of early-life adversity in the context of altered serotonin (5-HT; 5-hydroxytryptamine) system functioning in mice. The main body is focussing on a screening approach identifying molecular processes, potentially involved in distinct behavioural manifestations that emerge from or are concomitant with early adversity and, with regard to some behavioural manifestations, dependent on the functioning of the 5-HT system.},
  subject      = {Gehirn},
  language  = {en}
}
@phdthesis{Chowdhury2018,
  author    = {Chowdhury, Suvagata Roy},
  title     = {The Role of MicroRNAs in \(Chlamydia\) Infection},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-155866},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {The obligate intracellular pathogen Chlamydia trachomatis is the causative agent of trachoma related blindness and the sexually transmitted pelvic inflammatory disease. Being an obligate intracellular pathogen, C. trachomatis has an intricate dependency on the survival of the host cell. This relationship is indispensible owing to the fact that the pathogen spends a considerable fraction of its biphasic lifecycle within a cytoplasmic vacuole inside the host cell, the so-called chlamydial inclusion. The cellular apoptotic-signalling network is governed by several finely tuned regulatory cascades composed of pro- and anti-apoptotic proteins that respond to changes in the cellular homeostasis. In order to facilitate its intracellular survival, Chlamydia has been known to inhibit the premature apoptosis of the host cell via the stabilization of several host anti-apoptotic proteins such as cIAP2 and Mcl-1. While the pro- and anti-apoptotic proteins are the major regulators of the host apoptotic signalling network, a class of the small non-coding RNAs called microRNAs (miRNAs) has increasingly gained focus as a new level of regulatory control over apoptosis. This work investigates the changes in the host miRNA expression profile post Chlamydia infection using a high throughput miRNA deep sequencing approach. Several miRNAs previously associated with the modulation for apoptotic signalling were differentially expressed upon Chlamydia infection in human endothelial cells. Of the differentially regulated miRNAs, miR-30c-5p was of particular interest since it had been previously shown to target the tumor suppressor protein p53. Our lab and others have previously demonstrated that Chlamydia can downregulate the levels of p53 by promoting its proteasomal degradation. This work demonstrates that Chlamydia infection promotes p53 downregulation by increasing the abundance of miR-30c-5p and a successful infection cycle is hindered by a loss of miR-30c-5p. Over the last decade, dedicated research aimed towards a better understanding of apoptotic stimuli has greatly improved our grasp on the subject. While extrinsic stress, deprivation of survival signals and DNA damage are regarded as major proponents of apoptotic induction, a significant responsibility lies with the mitochondrial network of the cell. Mitochondrial function and dynamics are crucial to cell fate determination and dysregulation of either is decisive for cell survival and pathogenesis of several diseases. The ability of the mitochondrial network to perform its essential tasks that include ATP synthesis, anti-oxidant defense, and calcium homeostasis amongst numerous other processes critical to cellular equilibrium is tied closely to the fission and fusion of individual mitochondrial fragments. It is, thus, 8 unsurprising that mitochondrial dynamics is closely linked to apoptosis. In fact, many of the proteins involved regulation of mitochondrial dynamics are also involved in apoptotic signalling. The mitochondrial fission regulator, Drp1 has previously been shown to be transcriptionally regulated by p53 and is negatively affected by a miR- 30c mediated inhibition of p53. Our investigation reveals a significant alteration in the mitochondrial dynamics of Chlamydia infected cells affected by the loss of Drp1. We show that loss of Drp1 upon chlamydial infection is mediated by the miR-30c-5p induced depletion of p53 and results in a hyper-fused architecture of the mitochondrial network. While it is widely accepted that Chlamydia depends on the host cell metabolism for its intracellular growth and development, the role of mitochondria in an infected cell, particularly with respect to its dynamic nature, has not been thoroughly investigated. This work attempts to illustrate the dependence of Chlamydia on miR-30c-5p induced changes in the mitochondrial architecture and highlight the importance of these modulations for chlamydial growth and development.},
  subject      = {Chlamydienkrankheit},
  language  = {en}
}
@phdthesis{PradaSalcedo2018,
  author    = {Prada Salcedo, Juan Pablo},
  title     = {Image Processing and other bioinformatic tools for Neurobiology},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-157721},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {Neurobiology is widely supported by bioinformatics. Due to the big amount of data generated from the biological side a computational approach is required. This thesis presents four different cases of bioinformatic tools applied to the service of Neurobiology. The first two tools presented belong to the field of image processing. In the first case, we make use of an algorithm based on the wavelet transformation to assess calcium activity events in cultured neurons. We designed an open source tool to assist neurobiology researchers in the analysis of calcium imaging videos. Such analysis is usually done manually which is time consuming and highly subjective. Our tool speeds up the work and offers the possibility of an unbiased detection of the calcium events. Even more important is that our algorithm not only detects the neuron spiking activity but also local spontaneous activity which is normally discarded because it is considered irrelevant. We showed that this activity is determinant in the calcium dynamics in neurons and it is involved in important functions like signal modulation and memory and learning. The second project is a segmentation task. In our case we are interested in segmenting the neuron nuclei in electron microscopy images of c.elegans. Marking these structures is necessary in order to reconstruct the connectome of the organism. C.elegans is a great study case due to the simplicity of its nervous system (only 502 neurons). This worm, despite its simplicity has taught us a lot about neuronal mechanisms. There is still a lot of information we can extract from the c.elegans, therein lies the importance of reconstructing its connectome. There is a current version of the c.elegans connectome but it was done by hand and on a single subject which leaves a big room for errors. By automatizing the segmentation of the electron microscopy images we guarantee an unbiased approach and we will be able to verify the connectome on several subjects. For the third project we moved from image processing applications to biological modeling. Because of the high complexity of even small biological systems it is necessary to analyze them with the help of computational tools. The term in silico was coined to refer to such computational models of biological systems. We designed an in silico model of the TNF (Tumor necrosis factor) ligand and its two principal receptors. This biological system is of high relevance because it is involved in the inflammation process. Inflammation is of most importance as protection mechanism but it can also lead to complicated diseases (e.g. cancer). Chronic inflammation processes can be particularly dangerous in the brain. In order to better understand the dynamics that govern the TNF system we created a model using the BioNetGen language. This is a rule based language that allows one to simulate systems where multiple agents are governed by a single rule. Using our model we characterized the TNF system and hypothesized about the relation of the ligand with each of the two receptors. Our hypotheses can be later used to define drug targets in the system or possible treatments for chronic inflammation or lack of the inflammatory response. The final project deals with the protein folding problem. In our organism proteins are folded all the time, because only in their folded conformation are proteins capable of doing their job (with some very few exceptions). This folding process presents a great challenge for science because it has been shown to be an NP problem. NP means non deterministic Polynomial time problem. This basically means that this kind of problems cannot be efficiently solved. Nevertheless, somehow the body is capable of folding a protein in just milliseconds. This phenomenon puzzles not only biologists but also mathematicians. In mathematics NP problems have been studied for a long time and it is known that given the solution to one NP problem we could solve many of them (i.e. NP-complete problems). If we manage to understand how nature solves the protein folding problem then we might be able to apply this solution to many other problems. Our research intends to contribute to this discussion. Unfortunately, not to explain how nature solves the protein folding problem, but to explain that it does not solve the problem at all. This seems contradictory since I just mentioned that the body folds proteins all the time, but our hypothesis is that the organisms have learned to solve a simplified version of the NP problem. Nature does not solve the protein folding problem in its full complexity. It simply solves a small instance of the problem. An instance which is as simple as a convex optimization problem. We formulate the protein folding problem as an optimization problem to illustrate our claim and present some toy examples to illustrate the formulation. If our hypothesis is true, it means that protein folding is a simple problem. So we just need to understand and model the conditions of the vicinity inside the cell at the moment the folding process occurs. Once we understand this starting conformation and its influence in the folding process we will be able to design treatments for amyloid diseases such as Alzheimer's and Parkinson's. In summary this thesis project contributes to the neurobiology research field from four different fronts. Two are practical contributions with immediate benefits, such as the calcium imaging video analysis tool and the TNF in silico model. The neuron nuclei segmentation is a contribution for the near future. A step towards the full annotation of the c.elegans connectome and later for the reconstruction of the connectome of other species. And finally, the protein folding project is a first impulse to change the way we conceive the protein folding process in nature. We try to point future research in a novel direction, where the amino code is not the most relevant characteristic of the process but the conditions within the cell.},
  subject      = {Bildverarbeitung},
  language  = {en}
}
@phdthesis{Hampe2018,
  author    = {Hampe, Irene Aurelia Ida},
  title     = {Analysis of the mechanism and the regulation of histatin 5 resistance in \(Candida\) \(albicans\)},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-159634},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {Antimycotics such as fluconazole are frequently used to treat C. albicans infections of the oral mucosa. Prolonged treatment of the fungal infection with fluconazole pose a risk to resistance development. C. albicans can adapt to these stressful environmental changes by regulation of gene expression or by producing genetically altered variants that arise in the population. Adapted variants frequently carry activating mutations in zinc cluster transcription factors, which cause the upregulation of their target genes, including genes encoding efflux pumps that confer drug resistance. MDR1, regulated by the zinc cluster transcription factor Mrr1, as well as CDR1 and CDR2, regulated by the zinc cluster transcription factor Tac1, are well-known examples of genes encoding efflux pumps that extrude the antimycotic fluconazole from the fungal cell and thus contribute to the survival of the fungus. In this study, it was investigated if C. albicans can develop resistance to the antimicrobial peptide histatin 5, which serves as the first line of defence in the oral cavity of the human host. Recently, it was shown that C. albicans transports histatin 5 outside of the Candia cell via the efflux pump Flu1. As efflux pumps are often regulated by zinc cluster transcription factors, the Flu1 efflux pump could also be regulated by a zinc cluster transcription factor which could in a hyperactive form upregulate the expression of the efflux pump, resulting in increased export of histatin 5 and consequently in histatin 5 resistance. In order to find a zinc cluster transcription factor that upregulates FLU1 expression, a comprehensive library of C. albicans strains containing artificially activated forms of zinc cluster transcription factors was screened for suitable candidates. The screening was conducted on medium containing mycophenolic acid because mycophenolic acid is also a substrate of Flu1 and a strain expressing a hyperactive zinc cluster transcription factor that upregulates FLU1 expression should exhibit an easily recognisable mycophenolic acid-resistant phenotype. Further, FACS analysis, quantitative real-time RT-PCR analysis, broth microdilution assays as well as histatin 5 assays were conducted to analyse the mechanism and the regulation of histatin 5 resistance. Several zinc cluster transcription factors caused mycophenolic acid resistance and upregulated FLU1 expression. Of those, only hyperactive Mrr1 was able to confer increased histatin 5 resistance. Finding Mrr1 to confer histatin 5 resistance was highly interesting as fluconazole-resistant strains with naturally occurring Mrr1 gain of function mutations exist, which were isolated from HIV-infected patients with oral candidiasis. These Mrr1 gain of function mutations as well as artificially activated Mrr1 cause fluconazole resistance by upregulation of the efflux pump MDR1 and other target genes. In the course of the study, it was found that expression of different naturally occurring MRR1 gain-of-function mutations in the SC5314 wild type background caused increased FLU1 expression and increased histatin 5 resistance. The same was true for fluconazole-resistant clinical isolates with Mrr1 gain of function mutations, which also caused the overexpression of FLU1. Those cells were less efficiently killed by histatin 5 dependent on Mrr1. Surprisingly, FLU1 contributed only little to histatin 5 resistance, rather, overexpression of MDR1 mainly contributed to the Mrr1-mediated histatin 5 resistance, but also additional Mrr1-target genes were involved. These target genes are yet to be uncovered. Moreover, if a link between the yet unknown Mrr1-target genes contributing to fluconazole resistance and increased histatin 5 resistance can be drawn remains to be discovered upon finding of the responsible target genes. Collectively, this study contributes to the understanding of the impact of prolonged antifungal exposure on the interaction between host and fungus. Drug therapy can give rise to resistance evolution resulting in strains that have not only developed resistance to fluconazole but also to an innate host mechanism, which allows adaption to the host niche even in the absence of the drug.},
  subject      = {Histatin 5},
  language  = {en}
}
@phdthesis{Meister2018,
  author    = {Meister, Jonas},
  title     = {Wertigkeit operativer Stimmangleichung bei Mann-zu-Frau-Transsexualismus - Evaluation der Glottoplastik nach Wendler modifiziert durch Hagen},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-159201},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {Transsexualit{\"a}t ist gekennzeichnet durch die dauerhafte Gewissheit, in einem K{\"o}rper des falschen Geschlechts geboren worden zu sein. Bei Mann-zu-Frau-Transsexualit{\"a}t ist die Stimme ein oft untersch{\"a}tzter Bestandteil der ganzheitlichen Therapie. Kann mit konservativer Therapie kein zufriedenstellend weiblicher Stimmklang erreicht werden, ist Phonochirurgie die Methode der Wahl. In W{\"u}rzburg wird hierzu die Glottoplastik nach Wendler modifiziert durch Hagen angewendet. An der vorliegenden Studie zur Qualit{\"a}ts{\"u}berpr{\"u}fung des operativen Verfahrens nahmen insgesamt 21 auf diese Art operierte Patientinnen teil, von denen 18 zu einer Nachuntersuchung in W{\"u}rzburg erschienen und 3 die zugsandten Frageb{\"o}gen ausf{\"u}llten. Erwartet wurden eine Anhebung der mittleren Sprechstimmlage sowie eine Ver{\"a}nderung weiterer objektiver Stimmparameter. Mit einer angehobenen Sprechstimmlage wurde auch eine h{\"o}here Zufriedenheit der Patientinnen mit ihrer Stimme vermutet. Nach Erfahrungsberichten vieler Patientinnen blieben Probleme beim Telefonieren jedoch weiterhin bestehen. Diese f{\"u}r den subjektiven Therapieerfolg sehr wichtige Situation wurde mit einer Perzeptionsstudie gezielt untersucht. Insgesamt zeigte sich die Operation als risikoarme und effektive Therapieoption, um die mittlere Sprechstimmlage anzuheben. So lag die mittlere Sprechstimmlage der Patientinnen postoperativ im Median bei 170 Hz und somit im ausschließlich weiblichen Stimmlagenbereich. Die Anhebung der mittleren Sprechstimmlage ging mit einem leichten Verlust des Dynamikumfangs einher, der jedoch nur von ca. einem Drittel der Patientinnen als st{\"o}rend empfunden wurde. Zur subjektiven Erfolgskontrolle wurden Daten aus den standardisierten Frageb{\"o}gen „Voice Handicap Index" sowie „Fragebogen zur Lebenszufriedenheit" und dem eigenen „W{\"u}rzburger Fragebogen" erhoben und ausgewertet. Die Ergebnisse dieser Frageb{\"o}gen zeigten, abweichend von den guten objektiven Messwerten, deutliche Einschr{\"a}nkungen gegen{\"u}ber einer stimmgesunden Vergleichsgruppe aus der Literatur. Diese Defizite betrafen sowohl die stimmbezogenen Fragengebiete des Voice Handicap Index, als auch die allgemeine Lebenszufriedenheit. Dennoch gaben die Patientinnen an, durch die Stimmoperation ein selbstsichereres Auftreten gegen{\"u}ber fremden Personen gewonnen zu haben. Die subjektive Stimmzufriedenheit korrelierte sowohl mit der mittleren Sprechstimmlage als auch mit der Selbsteinsch{\"a}tzung der Weiblichkeit der Stimme. Bei Frequenz- und Dynamikumfang zeigten sich starke Differenzen zwischen objektiven Messergebnissen und subjektiver Zufriedenheit. F{\"u}r die Perzeptionsstudie zur Telefonsituation wurden von 18 Patientinnen sowie jeweils im Alter gepaarten m{\"a}nnlichen und weiblichen Kontrollsprechern identische Sprachaufnahmen angefertigt und in der Frequenz entsprechend der {\"U}bertragungs-bandbreite am Telefon bearbeitet. Diese Stimmproben wurden 50 m{\"a}nnlichen und 50 weiblichen zuf{\"a}llig ausgew{\"a}hlten Laienjuroren zur Bewertung hinsichtlich des Sprechergeschlechts vorgespielt. Gemessen wurde neben dem Urteil m{\"a}nnlich oder weiblich auch die Zeitspanne von Beginn der Wiedergabe bis zur Urteilseingabe. Ungef{\"a}hr 40 \% der transsexuellen Patientinnen wurden mehrheitlich, also in {\"u}ber 50 \% der Urteile als weiblich bewertet. Die Urteilszeit lag f{\"u}r die Sprachproben der transsexuellen Patientinnen signifikant {\"u}ber der Urteilszeit f{\"u}r m{\"a}nnliche und weibliche Kontrollsprecher. Bezogen auf die Juroren zeigten sich Unterschiede zwischen m{\"a}nnlicher und weiblicher Jurorengruppe: M{\"a}nner ordneten die Sprachproben h{\"a}ufiger einem weiblichen Sprecher zu. Weibliche Juroren f{\"a}llten ihr Urteil hingegen signifikant schneller als m{\"a}nnliche Juroren. Es zeigte sich eine positive Korrelation der Geschlechtszuordnung mit der mittleren Sprechstimmlage. Die unabh{\"a}ngig von der Sprechstimmlage deutlich verl{\"a}ngerte Urteilszeit f{\"u}r transsexuelle Sprecherinnen zeigte jedoch, dass neben der mittleren Sprechstimmlage auch noch andere Faktoren die Geschlechtszuordnung beeinflussen. Dementsprechend existierte keine klare Grenzfrequenz, oberhalb derer Stimmen regelhaft als weiblich wahrgenommen wurden. Auch in einem in der Literatur mehrfach als ausschließlich weiblich definierten Sprechbereich wurden die Stimmen einzelner Patientinnen mehrheitlich als m{\"a}nnlich wahrgenommen. Es konnte kein Zusammenhang der Formantfrequenzen F1 - F3 mit der Geschlechtszuordnung gefunden werden. Zusammenfassend zeigten diese aus objektiven Stimmdaten, Eigen- und Fremd-bewertung bestehenden Ergebnisse, dass durch alleinige Operation zwar eine h{\"o}here Stimmlage, jedoch kein vollst{\"a}ndig weiblicher Stimmklang erreicht wurde. Deswegen muss die Phonochirurgie zuk{\"u}nftig st{\"a}rker in ein umfassendes Behandlungskonzept aus logop{\"a}dischem Stimmtraining, {\"U}bungen f{\"u}r eine weibliche Gestik und Mimik sowie Alltagstraining eingebunden werden. Hierzu wurde in dieser Arbeit ein neuer Behandlungsalgorithmus f{\"u}r die Univ.-HNO-Klinik W{\"u}rzburg erstellt.},
  subject      = {Transsexualismus},
  language  = {de}
}
@phdthesis{Appeltshauser2018,
  author    = {Appeltshauser, Luise Theresia},
  title     = {Detektion und Charakterisierung von Autoantik{\"o}rpern gegen paranodale Proteine bei Patienten mit inflammatorischer Polyneuropathie},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-169457},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {K{\"u}rzlich wurden bei immunvermittelten Neuropathien Autoantik{\"o}rper gegen Proteine des paranodalen axoglialen Komplexes beschrieben. Deren Charakteristika, Pr{\"a}valenzen, pathophysiologische Relevanz sowie Bedeutung f{\"u}r Diagnostik und Therapie sind jedoch noch nicht abschließend erforscht. In dieser Studie wurden daher Seren und Plasmapheresematerial (PE-Material) von 150 Patienten mit inflammatorischen Neuropathien, n{\"a}mlich 105 mit chronisch inflammatorischer demyelinisierender Polyneuropathie (CIDP), 21 mit Guillain- Barr{\´e}-Syndrom (GBS) und 24 mit multifokaler motorischer Neuropathie (MMN), welche etablierte diagnostische Kriterien der jeweiligen Krankheit erf{\"u}llen, sowie 74 Kontrollen mittels immunhistochemischen F{\"a}rbungen an murinen Zupfnervenpr{\"a}paraten und/oder ELISA (Enzyme-linked Immunosorbent Assay) auf Autoantik{\"o}rper gegen die paranodalen Proteine Caspr, Contactin-1 und Neurofascin- 155 untersucht. Bei positivem Ergebnis wurde deren Spezifit{\"a}t mittels immunhistochemischen F{\"a}rbungen an transfizierten HEK (Human embryonic kidney)- 293-Zellen und Pr{\"a}inkubationsversuchen best{\"a}tigt. Es wurden die IgG-Subklassen und die Antik{\"o}rpertiter bestimmt und das Komplementbindungsverhalten unter Zugabe von intraven{\"o}sen Immunglobulinen (IVIG) mit zellbasierten und ELISA-basierten Methoden analysiert. Klinische Merkmale und das Therapieansprechen Antik{\"o}rper-positiver Patienten wurden ermittelt und mit den experimentellen Ergebnissen in Zusammenhang gesetzt. IgG-Autoantik{\"o}rper gegen Contactin-1 konnten bei vier Patienten mit CIDP nachgewiesen werden, IgG-Autoantik{\"o}rper gegen Caspr bei einem Patienten mit CIDP und einer Patientin mit GBS. Es konnten keine weiteren Autoantik{\"o}rper bei CIDP-Patienten, GBS-Patienten, MMN-Patienten oder bei den Kontrollen detektiert werden. Die Pr{\"a}valenz von Autoantik{\"o}rpern gegen axogliale paranodale Proteine liegt somit in dieser Studie bei jeweils 4,76\% bei CIDP und GBS und 0\% bei MMN. Die Antik{\"o}rper geh{\"o}rten bei Patienten in der akuten Erkrankungsphase (zwei der CIDP-Patienten mit Anti-Contactin-1-Autoantik{\"o}rpern und eine GBS-Patientin mit Anti-Caspr-Autoantik{\"o}rpern) haupts{\"a}chlich den Subklassen IgG1 und IgG3 an, bei Patienten in der chronischen Phase (zwei der CIDP-Patienten mit Anti-Contactin-1-Autoantik{\"o}rpern, ein CIDP-Patient mit Anti-Caspr-Autoantik{\"o}rpern) {\"u}berwog die Subklasse IgG4. Experimentell kam es zur Komplementbindung und -aktivierung abh{\"a}ngig vom Gehalt der Subklassen IgG1-3, nicht aber IgG4; diese konnte durch die Zugabe von IVIG dosisabh{\"a}ngig gemindert werden. Alle Autoantik{\"o}rper-positiven CIDP-Patienten zeigten einen GBS-artigen Beginn mit einer schweren motorischen Beteiligung. Anti-Contactin-1-positive Patienten kennzeichnete klinisch zus{\"a}tzlich das Vorkommen einer Ataxie und eines Tremors, Anti-Caspr-positive Patienten das Vorkommen starker neuropathischer Schmerzen. Elektrophysiologisch standen neben Hinweisen auf eine Leitungsst{\"o}rung Zeichen einer axonalen Sch{\"a}digung im Vordergrund. Als histopathologisches Korrelat lagen eine nodale Architekturst{\"o}rung und ein Axonverlust vor. Die Patienten zeigten nur in der Anfangsphase der Erkrankung ein Ansprechen auf IVIG. Bei drei CIDP-Patienten mit IgG4-Autoantik{\"o}rpern (zwei Patienten mit Anti-Contactin-1-Antik{\"o}rpern und ein Patient mit Anti-Caspr-Antik{\"o}rpern) wurde eine Therapie mit Rituximab durchgef{\"u}hrt. Diese f{\"u}hrte zu einer Titerreduktion und zur zeitgleichen klinischen und elektrophysiologischen Befundbesserung bei zwei Patienten. Die in dieser Arbeit angewandten Screeningmethoden f{\"u}hrten zum erfolgreichen Nachweis von Autoantik{\"o}rpern gegen paranodale axogliale Proteine. Die Patienten mit positivem Autoantik{\"o}rpernachweis definieren eine kleine Untergruppe mit {\"a}hnlichen klinischen Merkmalen im Kollektiv der Patienten mit inflammatorischen Polyneuropathien. Histopathologische Merkmale sowie das Therapieansprechen auf antik{\"o}rperdepletierende Therapie sprechen in Kombination mit den Ergebnissen weiterer Studien zu paranodalen Autoantik{\"o}rpern f{\"u}r eine pathogenetische Relevanz der Autoantik{\"o}rper. Mit einem charakteristischen, am Schn{\"u}rring ansetzenden Pathomechanismus k{\"o}nnten Neuropathien mit Nachweis von paranodalen Autoantik{\"o}rpern der k{\"u}rzlich eingef{\"u}hrten Entit{\"a}t der Nodo-Paranodopathien angeh{\"o}ren. Die Komplementaktivierung und das Therapieansprechen der Patienten auf IVIG stehen m{\"o}glicherweise in Zusammenhang mit der pr{\"a}dominanten IgG-Subklasse. Diese k{\"o}nnte auch in Bezug auf die Chronifizierung eine Rolle spielen. Der Nachweis von Autoantik{\"o}rpern gegen paranodale Proteine hat wohlm{\"o}glich in Zukunft direkte Konsequenzen auf das diagnostische und therapeutische Prozedere bei Patienten mit CIDP und GBS; weitere klinische und experimentelle Daten aus gr{\"o}ßeren, prospektiven Studien sind jedoch zum weiteren Verst{\"a}ndnis und zur Charakterisierung dieser Entit{\"a}t notwendig.},
  subject      = {Polyneuropathie},
  language  = {de}
}
@phdthesis{Muehlemann2018,
  author    = {M{\"u}hlemann, Markus},
  title     = {Intestinal stem cells and the Na\(^+\)-D-Glucose Transporter SGLT1: potential targets regarding future therapeutic strategies for diabetes},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-169266},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {The pancreas and the small intestine are pivotal organs acting in close synergism to regulate glucose metabolism. After absorption and processing of dietary glucose within the small intestine, insulin and glucagon are released from pancreatic islet cells to maintain blood glucose homeostasis. Malfunctions affecting either individual, organ-specific functions or the sophisticated interplay of both organs can result in massive complications and pathologic conditions. One of the most serious metabolic diseases of our society is diabetes mellitus (DM) that is hallmarked by a disturbance of blood glucose homeostasis. Type 1 (T1DM) and type 2 (T2DM) are the main forms of the disease and both are characterized by chronic hyperglycemia, a condition that evokes severe comorbidities in the long-term. In the past, several standard treatment options allowed a more or less adequate therapy for diabetic patients. Albeit there is much effort to develop new therapeutic interventions to treat diabetic patients in a more efficient way, no cure is available so far. In view of the urgent need for alternative treatment options, a more systemic look on whole organ systems, their biological relation and complex interplay is needed when developing new therapeutic strategies for DM. T1DM is hallmarked by an autoimmune-mediated destruction of the pancreatic β-cell mass resulting in a complete lack of insulin that is in most patients restored by applying a life-long recombinant insulin therapy. Therefore, novel regenerative medicine-based concepts focus on the derivation of bioartificial β-like cells from diverse stem cell sources in vitro that survive and sustain to secrete insulin after implantation in vivo. In this context, the first part of this thesis analyzed multipotent intestinal stem cells (ISCs) as alternative cell source to derive bioartificial, pancreatic β-like cells in vitro. From a translational perspective, intestinal stem cells pose a particularly attractive cell source since intestinal donor tissues could be obtained via minimal invasive endoscopy in an autologous way. Furthermore, intestinal and pancreatic cells both derive from the same developmental origin, the endodermal gut tube, favoring the differentiation process towards functional β-like cells. In this study, pancreas-specific differentiation of ISCs was induced by the ectopic expression of the pancreatic transcription factor 1 alpha (Ptf1a), a pioneer transcriptional regulator of pancreatic fate. Furthermore, pancreatic lineage-specific culture media were applied to support the differentiation process. In general, ISCs grow in vitro in a 3D Matrigel®-based environment. Therefore, a 2D culture platform for ISCs was established to allow delivery and ectopic expression of Ptf1a with high efficiency. Next, several molecular tools were applied and compared with each other to identify the most suitable technology for Ptf1a delivery and expression within ISCs as well as their survival under the new established 2D conditions. Success of differentiation was investigated by monitoring changes in cellular morphology and induction of pancreatic differentiation-specific gene expression profiles. In summary, the data of this project part suggest that Ptf1a harbors the potential to induce pancreatic differentiation of ISCs when applying an adequate differentiation media. However, gene expression analysis indicated rather an acinar lineage-determination than a pancreatic β-cell-like specification. Nevertheless, this study proved ISCs not only as interesting stem cell source for the generation of pancreatic cell types with a potential use in the treatment of T1DM but alsoPtf1a as pioneer factor for pancreatic differentiation of ISCs in general. Compared to T1DM, T2DM patients suffer from hyperglycemia due to insulin resistance. In T2DM management, the maintenance of blood glucose homeostasis has highest priority and can be achieved by drugs affecting the stabilization of blood glucose levels. Recent therapeutic concepts are aiming at the inhibition of the intestinal glucose transporter Na+-D-Glucose cotransporter 1 (SGLT1). Pharmacological inhibition of SGLT1 results in reduced postprandial blood glucose levels combined with a sustained and increased Glucagon-like peptide 1 (GLP-1) secretion. So far, systemic side effects of this medication have not been addressed in detail. Of note, besides intestinal localization, SGLT1 is also expressed in various other tissues including the pancreas. In context of having a closer look also on the interplay of organs when developing new therapeutic approaches for DM, the second part of this thesis addressed the effects on pancreatic islet integrity after loss of SGLT1. The analyses comprised the investigation of pancreatic islet size, cytomorphology and function by the use of a global SGLT1 knockout (SGLT1-/-) mouse model. As SGLT1-/- mice develop the glucose-galactose malabsorption syndrome when fed a standard laboratory chow, these animals derived a glucose-deficient, fat-enriched (GDFE) diet. Wildtype mice on either standard chow (WTSC) or GDFE (WTDC) allowed the discrimination between diet- and knockout-dependent effects. Notably, GDFE fed mice showed decreased expression and function of intestinal SGLT1, while pancreatic SGLT1 mRNA levels were unaffected. Further, the findings revealed increased isled sizes, reduced proliferation- and apoptosis rates as well as an increased α-cell and reduced β-cell proportion accompanied by a disturbed cytomorphology in islets when SGLT1 function is lost or impaired. In addition, pancreatic islets were dysfunctional in terms of insulin- and glucagon-secretion. Moreover, the release of intestinal GLP-1, an incretin hormone that stimulates insulin-secretion in the islet, was abnormal after glucose stimulatory conditions. In summary, these data show that intestinal SGLT1 expression and function is nutrient dependent. The data obtained from the islet studies revealed an additional and new role of SGLT1 for maintaining pancreatic islet integrity in the context of structural, cytomorphological and functional aspects. With special emphasis on SGLT1 inhibition in diabetic patients, the data of this project indicate an urgent need for analyzing systemic side effects in other relevant organs to prove pharmacological SGLT1 inhibition as beneficial and safe. Altogether, the findings of both project parts of this thesis demonstrate that focusing on the molecular and cellular relationship and interplay of the small intestine and the pancreas could be of high importance in context of developing new therapeutic strategies for future applications in DM patients.},
  subject      = {Stammzelle},
  language  = {en}
}
@phdthesis{Rehman2018,
  author    = {Rehman, Saba},
  title     = {Identification of accessible and closed substrate binding sites in the outward open cleft of rat Organic Cation Transporter 1 (rOCT1)},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-169992},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {The present study was conducted on the rOCT1, a member of SLC22 family. Structurally, it consists of 12 membrane spanning α-helices with both N- and C-termini intracellular. Studies done so far, through tracer uptake and inhibition, reconstitution of rOCT1 in nanodiscs and proteoliposomes and voltage-clamp fluorometry, have identified the main amino acids in the cleft of rOCT1 that interact in a critical manner with the substrates/inhibitors either directly or indirectly. Homology modeling studies have also supported these observations. In the present study we aimed at measuring the binding of substrates MPP+ and TEA+ to rOCT1 at 0oC in order to establish the amino acids in the cleft region that interact with the substrate when the transporter is frozen in the outward-open conformation. Previously identified crucial amino acids (Asp475, Phe160, Leu447, Arg440, Trp218 and Tyr222) were selected for the study. rOCT1 wild-type and its mutants were stably expressed in HEK293 cells and these cells were used for the binding measurements with the radioactive substrate (MPP+ or TEA+) at 0°C in Mg-Ca-PBS buffer as described in "Materials and Methods" section in detail. rOCT1 wild-type revealed for MPP+-binding a KD which was not significantly different from the corresponding Km value. Also, after addition of 10 nM non-radioactive MPP+, an initial increase of about 20\% in bound MPP+ was observed. The results indicate that the Km for transport is dependent on the binding of MPP+ to the outward-open conformation and hints at the possibility of allosteric interaction between the binding sites. Mutations at position Trp218, Phe160 and Asp475 resulted in a change in the KD value. Trp218 mutations also showed an allosteric increase similar to the rOCT1 wild-type. This study suggests that these amino acids are located at a critical position in the outward-open conformation for MPP+ transport. TEA+-binding could not be observed in rOCT1 wild-type, indicating that the binding site is perhaps inaccessible for TEA+ in frozen outward-open state. The mutants D475E, F160A, L447F, R440K and Y222F showed a very low affinity binding with a very high KD value as compared to the corresponding Km values indicating that the transporter might have different affinities for extra-cellular binding alone and for the complete transport process especially if temperature is the limiting factor. Substrate inhibition studies done using both MPP+ and TEA+ have confirmed the existence of overlapping binding sites for these two ligands. This study has confirmed the direct interaction of Trp218, Phe160, Asp475 with MPP+ and Phe160, Asp475, Leu447, Arg440 and Tyr222 with TEA+ in the outward-open conformation.},
  subject      = {Kation},
  language  = {en}
}
@phdthesis{CabelloGonzalez2018,
  author    = {Cabello Gonz{\´a}lez, Victoria},
  title     = {From behavioral to neurobiological characterization of Rsk2 knockout mice as an animal model for Coffin-Lowry syndrome},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-171275},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {Coffin-Lowry syndrome is a rare syndromic form of X-linked mental retardation caused by heterogeneous loss-of-function mutations in the gene RPS6KA3 that encodes the RSK2 protein. Clinical features are delayed motor development, small height, progressive skeletal malformations and mental retardation. Rsk2 deficiency affects behavioral, cellular and molecular functions. To characterize and investigate how this deficiency affects these functions, we made a series of experiments using Rsk2-deficient mice as the animal model for Coffin-Lowry syndrome. We applied a battery of behavioral tests and included the use of the IntelliCage for the first time as a behavioral paradigm to study anxiety-like behavior and depression-like behavior in Rsk2-deficient mice. Results from the conventional behavioral tests and from the IntelliCage indicate that Rsk2-deficient mice may have an anti-anxiety and anti-depressive phenotype. We evaluated in Rsk2 deficient mice the relative gene expression of a set of genes coding for proteins related to RSK2 which are involved in fear memory, synaptic plasticity, neurogenesis, learning, emotional behavior and stress. We found gene expression alterations in the prefrontal cortex and striatum. These results suggest that RSK2 may be involved in the expression of the genes. RSK2 is known to be related to monoamine neurotransmitter function. We measured the levels of dopamine, serotonin and noradrenaline/norepinephrine and their metabolites in different brain regions of Rsk2-deficient mice. We found differences in the dopaminergic and noradrenergic systems suggesting an increased or decreased activity of these neurotransmission systems as a result of Rsk2 deficiency. Adult neurogenesis is a form of neuronal plasticity and a multi-step process of cell development. We explored if this form of neuronal plasticity was affected by Rsk2-deficiency. Our results indicate that adult hippocampal neurogenesis is not influenced by lifelong Rsk2 deficiency. It would be worth to analyze in the future other aspects of neuroplasticity. We have confirmed, that behavioral characteristics of Rsk2-deficient mice make them an interesting model to study the Coffin-Lowry syndrome by extending the behavioral characterization on the emotional level. Furthermore, we have extended the characterization of the model on a molecular level, opening new opportunities to study and understand the pathophysiological basis of the Coffin-Lowry syndrome.},
  subject      = {Knockout <Molekulargenetik>},
  language  = {en}
}
@phdthesis{Wedel2018,
  author    = {Wedel, Carolin},
  title     = {The impact of DNA sequence and chromatin on transcription in \(Trypanosoma\) \(brucei\)},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-173438},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {For cellular viability, transcription is a fundamental process. Hereby, the DNA plays the most elemental and highly versatile role. It has long been known that promoters contain conserved and often well-defined motifs, which dictate the site of transcription initiation by providing binding sites for regulatory proteins. However, research within the last decade revealed that it is promoters lacking conserved promoter motifs and transcribing constitutively expressed genes that constitute the majority of promoters in eukaryotes. While the process of transcription initiation is well studied, whether defined DNA sequence motifs are required for the transcription of constitutively expressed genes in eukaryotes remains unknown. In the highly divergent protozoan parasite Trypanosoma brucei, most of the proteincoding genes are organized in large polycistronic transcription units. The genes within one polycistronic transcription unit are generally unrelated and transcribed by a common transcription start site for which no RNA polymerase II promoter motifs have been identified so far. Thus, it is assumed that transcription initiation is not regulated but how transcription is initiated in T. brucei is not known. This study aimed to investigate the requirement of DNA sequence motifs and chromatin structures for transcription initiation in an organism lacking transcriptional regulation. To this end, I performed a systematic analysis to investigate the dependence of transcription initiation on the DNA sequence. I was able to identify GT-rich promoter elements required for directional transcription initiation and targeted deposition of the histone variant H2A.Z, a conserved component during transcription initiation. Furthermore, nucleosome positioning data in this work provide evidence that sites of transcription initiation are rather characterized by broad regions of open and more accessible chromatin than narrow nucleosome depleted regions as it is the case in other eukaryotes. These findings highlight the importance of chromatin during transcription initiation. Polycistronic RNA in T. brucei is separated by adding an independently transcribed miniexon during trans-splicing. The data in this work suggest that nucleosome occupancy plays an important role during RNA maturation by slowing down the progressing polymerase and thereby facilitating the choice of the proper splice site during trans-splicing. Overall, this work investigated the role of the DNA sequence during transcription initiation and nucleosome positioning in a highly divergent eukaryote. Furthermore, the findings shed light on the conservation of the requirement of DNA motifs during transcription initiation and the regulatory potential of chromatin during RNA maturation. The findings improve the understanding of gene expression regulation in T. brucei, a eukaryotic parasite lacking transcriptional Regulation.},
  subject      = {Transkription},
  language  = {en}
}
@phdthesis{Schreiber2018,
  author    = {Schreiber, Benjamin},
  title     = {Selective and enhanced fluorescence by biocompatible nanocoatings to monitor G-protein-coupled receptor dynamics},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-173923},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {Fluorescence microscopy has become one of the most important techniques for the imaging of biological cells and tissue, since the technique allows for selective labeling with fluorescent molecules and is highly suitable for low-light applications down to the single molecule regime. The methodological requirements are well-defined for studying membrane receptors within a highly localized nanometer-thin membrane. For example, G-protein-coupled receptors (GPCRs) are an extensively studied class of membrane receptors that represent one of the most important pharmaceutical targets. Ligand binding and GPCR activation dynamics are suspected to take place at the millisecond scale and may even be far faster. Thus, techniques that are fast, selective, and live-cell compatible are required to monitor GPCR dynamics. Fluorescence resonance energy transfer (FRET) and total internal reflection fluorescence microscopy (TIRF-M) are methods of choice to monitor the dynamics of GPCRs selectively within the cell membrane. Despite the remarkable success of these modalities, there are limitations. Most importantly, inhomogeneous illumination can induce imaging artifacts, rendering spectroscopic evaluation difficult. Background signal due to scattering processes or imperfect labeling can hamper the signal-to-noise, thus limiting image contrast and acquisition speed. Careful consideration of the internal physiology is required for FRET sensor design, so that ligand binding and cell compatibility are well-preserved despite the fluorescence labeling procedures. This limitation of labeling positions leads to very low signal changes in FRET-based GPCR analysis. In addition, microscopy of these systems becomes even more challenging in single molecule or low-light applications where the accuracy and temporal resolution may become dramatically low. Fluorescent labels should therefore be brighter, protected from photobleaching, and as small as possible to avoid interference with the binding kinetics. The development of new fluorescent molecules and labeling methods is an ongoing process. However, a complete characterization of new labels and sensors takes time. So far, the perfect dye system for GPCR studies has not been found, even though there is high demand. Thus, this thesis explores and applies a different approach based on improved illumination schemes for TIRF-M as well as metal-coated coverslips to enhance fluorescence and FRET efficiency. First, it is demonstrated that a 360° illumination scheme reduces typical TIRF artifacts and produces a much more homogenously illuminated field of view. Second, membrane imaging and FRET spectroscopy are improved by metal coatings that are used to modulate the fluorescent properties of common fluorescent dyes. Computer simulation methods are used to understand the underlying photophysics and to design the coatings. Third, this thesis explores the operational regime and limitations of plasmonic approaches with high sectioning capabilities. The findings are summarized by three publications that are presented in the results section of this work. In addition, the theory of fluorescence and FRET is explained, with particular attention to its emission modulations in the vicinity of metal-dielectric layers. Details of the instrumentation, computer simulations, and cell culture are described in the method section. The work concludes with a discussion of the findings within the framework of recent technological developments as well as perspectives and suggestions for future approaches complete the presented work.},
  subject      = {G-Protein gekoppelte Rezeptoren},
  language  = {en}
}
@phdthesis{Confalonieri2018,
  author    = {Confalonieri, Davide},
  title     = {Development and characterization of a bone marrow stem cell niche model},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-163128},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {Kritische Knochendefekte stellen heutzutage ein ungel{\"o}stes Problem in der klinischen Praxis dar, da die verf{\"u}gbaren prothetischen Optionen oft die mechanische Anpassung an das Gewebe nicht gew{\"a}hrleisten oder zu wichtigen immunologischen und Implantat-bedingten Komplikationen f{\"u}hren. In diesem Kontext erm{\"o}glichen Tissue Engineering-Ans{\"a}tze neue Strategien, um in vitro Zell-Material Interaktionen zu untersuchen und so die Implantatmaterialien zu optimieren. In dieser Arbeit habe ich Zell-Material Interaktionen eines neuen Kollagen-basierten Scaffolds untersucht, das langfristig als Tr{\"a}gerstruktur f{\"u}r eine zellbasierte Therapie f{\"u}r kritische Knochendefekte entwickelt werden soll. Im Rahmen der Dissertation konnte ich belegen, dass die Kollagen-basierten makropor{\"o}se Mikrocarrier f{\"u}r die Zellvermehrung humaner mesenchymaler Stammzellen (MSC) und deren osteogene Differenzierung unter GMP Bedingungen verwendet werden k{\"o}nnen. Außerdem habe ich die die Kokultur von h{\"a}matopoietischen Stammzellen des Knochenmarks und multiplen Myelomzellen funktionell charakterisiert. Ich konnte erstmals Kulturbedingungen etablieren, die die Langzeitkultur ohne die Verwendung von Zytokinen erm{\"o}glicht. Mittels dieser Kokultur konnte ich ein Knochenmarknischen-Modell etablieren und die Untersuchung der Expression von zentralen Signalkaskaden der Hom{\"o}ostase dieser Nische untersuchen. Ich konnte die Expression von zwei verschiedenen Isoformen von Osteopontin nachweisen, die in Tiermodellen nicht gefunden werden. Diese Isoformen des Osteopontins habe ich kloniert und die rekombinanten Isoformen exprimiert und ihre Rollen in der Hom{\"o}ostase der Knochenmarknische untersucht. Critical size bone defects represent nowadays an unresolved problem in the clinical practice, where the available prosthetic options often lack adequate mechanical matching to the host tissue or lead to important immunological and implant-related complications. In this context, Tissue Engineering approaches promise more effective strategies to study cell-material interactions in vitro and consequently optimize implant materials. In this work, I investigated the cell-scaffold interactions of a new collagen-based scaffold for a putative cell-based therapy for critical size defects to be developed. In the context of this thesis, I could demonstrate that the collagen-based macroporous microcarriers could be employed for the expansion and osteogenic differentiation of human mesenchymal stromal cells (MSCs) under GMP-compliant conditions. Moreover, I functionally characterized the co-culture of bone marrow hematopoietic stem cells and multiple myeloma cells. I was for the first time able to establish culture conditions allowing their long-term culture in absence of externally supplemented cytokines. Using this co-culture, I was able to establish a bone marrow niche model to investigate the expression of key signaling pathways involved in the niche´s homeostasis. I was able to demonstrate the expression of two different isoforms of Osteopontin, that could not previously be detected in animal models. Finally, I cloned these Osteopontin isoforms, expressed recombinant versions of the isoforms, and investigated their roles in the homeostasis of the bone marrow niche.},
  subject      = {bone marrow niche},
  language  = {en}
}
@phdthesis{Dejure2018,
  author    = {Dejure, Francesca Romana},
  title     = {Investigation of the role of MYC as a stress responsive protein},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-158587},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {The transcription factor MYC is deregulated in over 70\% of all human tumors and, in its oncogenic form, plays a major role in the cancer metabolic reprogramming, promoting the uptake of nutrients in order to sustain the biosynthetic needs of cancer cells. The research presented in this work aimed to understand if MYC itself is regulated by nutrient availability, focusing on the two major fuels of cancer cells: glucose and glutamine. Initial observations showed that endogenous MYC protein levels strongly depend on the availability of glutamine, but not of glucose. Subsequent analysis highlighted that the mechanism which accounts for the glutamine-mediated regulation of MYC is dependent on the 3´-untranslated region (3´-UTR) of MYC. Enhanced glutamine utilization by tumors has been shown to be directly linked to MYC oncogenic activity and MYC-dependent apoptosis has been observed under glutamine starvation. Such effect has been described in experimental systems which are mainly based on the use of MYC transgenes that do not contain the 3´-UTR. It was observed in the present study that cells are able to survive under glutamine starvation, which leads to cell cycle arrest and not apoptosis, as previously reported. However, enforced expression of a MYC transgene, which lacks the 3´-UTR, strongly increases the percentage of apoptotic cells upon starvation. Evaluation of glutamine-derived metabolites allowed to identify adenosine nucleotides as the specific stimulus responsible for the glutamine-mediated regulation of MYC, in a 3´-UTR-dependent way. Finally, glutamine-dependent MYC-mediated effects on RNA Polymerase II (RNAPII) function were evaluated, since MYC is involved in different steps of global transcriptional regulation. A global loss of RNAPII recruitment at the transcriptional start site results upon glutamine withdrawal. Such effect is overcome by enforced MYC expression under the same condition. This study shows that the 3´UTR of MYC acts as metabolic sensor and that MYC globally regulates the RNAPII function according to the availability of glutamine. The observations presented in this work underline the importance of considering stress-induced mechanisms impinging on the 3´UTR of MYC.},
  subject      = {Myc},
  language  = {en}
}
@phdthesis{Froehlich2018,
  author    = {Fr{\"o}hlich, Monika Gabriele},
  title     = {Die Bedeutung von CD28 vermittelter Kostimulation f{\"u}r CD8 T-Zell-Ged{\"a}chtnisreaktionen},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-158791},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {Immunologische Ged{\"a}chtnisreaktionen sind die Grundlage um wiederkehrende Erreger schnell und effizient zu bek{\"a}mpfen und um einen Impfschutz zu generieren. Das zellvermittelte Ged{\"a}chtnis wird unter anderem durch CD8 Ged{\"a}chtnis-T-Zellen aufgebaut, welche vor allem im Kontext von Immunreaktionen gegen intrazellul{\"a}rer Erreger vonn{\"o}ten sind, um bei Reinfektion mit den Erregerst{\"a}mmen einen schnellen Schutz zu gew{\"a}hrleisten. Ein detailliertes Wissen {\"u}ber die Generierung, Kontrolle und Reaktivierung der Ged{\"a}chtniszellen ist n{\"u}tzlich, um Ged{\"a}chtnisreaktionen verstehen und lenken zu k{\"o}nnen. Durch die Entdeckung des TZR und CD28 wurden Meilensteine f{\"u}r das Verst{\"a}ndnis der T-Zellaktivierung gelegt und die Grundlage geschaffen, CD8 Ged{\"a}chtnisreaktionen zu verstehen. Auch wenn f{\"u}r prim{\"a}re Immunreaktionen die „2-Signal-Theorie" lange als erwiesen gilt, so blieb die Rolle der Kostimulation f{\"u}r Ged{\"a}chtnisreaktionen lange umstritten. In dieser Arbeit wurden verschiedene methodische Herangehensweisen verwendet, mit denen durchgehend die Bedeutung von CD28 vermittelter Kostimulation f{\"u}r immunologische CD8 T-Zell-Ged{\"a}chtnisreaktionen nachgewiesen wurde. CD28 blockierende Antik{\"o}rper und CD28 induzierbar deletierbare Mauslinien wurden im Modellinfektionssystem mit Ovalbumin produzierenden Listeria monocytogenes zur Analyse der Prim{\"a}r- und Sekund{\"a}rantworten verwendet. Mit diesen Methoden konnte eine Beeintr{\"a}chtigung der Expansion von CD8 Ged{\"a}chtniszellen in Abwesenheit von CD28 bewiesen werden. Weiterhin werden Effektorfunktionen wie Degranulation und Produktion von IFN-γ w{\"a}hrend der Sekund{\"a}rinfektion in Abwesenheit von Kostimulation eingeschr{\"a}nkt. Mit Hilfe von Experimenten, bei denen CD28 suffizienten M{\"a}usen eine geringe Anzahl an naiven, antigenspezifischen, CD28 deletierbaren CD8 T-Zellen transferiert wurden, wurde die Bedeutung der Kostimulation f{\"u}r die Expansion von Ged{\"a}chtniszellen best{\"a}tigt, jedoch konnte {\"u}berraschenderweise auch ein Anstieg der Effektorfunktionen in Abwesenheit von CD28 sowohl w{\"a}hrend der Prim{\"a}r- als auch der Sekund{\"a}rantwort dokumentiert werden. Diese zur globalen Blockade bzw. Deletion widerspr{\"u}chlichen Ergebnisse lassen eine Beteiligung anderer CD28 abh{\"a}ngiger Zelltypen an der Induktion der Effektorfunktionen der CD8 T-Zellen plausibel erscheinen, wie zum Beispiel Einfl{\"u}sse von T-Helferzellen, welche die Effektorfunktionen positiv verst{\"a}rken, solange sie selbst Kostimulationssignale empfangen k{\"o}nnen. Weiterhin konnte gezeigt werden, dass sich Ged{\"a}chtniszellen an den CD28 defizienten Ph{\"a}notyp - eine CD28 intakte immunologische Umgebung vorausgesetzt - adaptieren k{\"o}nnen, wenn ausreichend Zeit nach Deletion und vor Sekund{\"a}rinfektion verstreichen konnte.},
  subject      = {Antigen CD28},
  language  = {de}
}
@phdthesis{GilPulido2018,
  author    = {Gil Pulido, Jes{\´u}s},
  title     = {The role of Batf3-dependent dendritic cells and the IL-23 receptor in atherosclerosis},
  doi       = {10.25972/OPUS-16720},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-167203},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {Cardiovascular diseases represent the leading cause of death worldwide, with myocardial infarction and strokes being the most common complications. In both cases, the appearance of an enlarged artery wall as a consequence of a growing plaque is responsible for the disturbance of the blood flow. The formation of plaques is driven by a chronic inflammatory condition known as atherosclerosis, characterized by an initial step of endothelial cell (EC) dysfunction followed by the recruitment of circulating immune cells into the tunica intima of the vessel. Accumulation of lipids and cells lead to the formation of atheromatous plaques that will define the cardiovascular outcome of an individual. The role of the immune system in the progression of atherosclerosis has been widely recognized. By far, macrophages constitute the most abundant cell type in lesions and are known to be the major source of the lipid-laden foam cell pool during the course of the disease. However, other immune cells types, including T cells, dendritic cells (DCs) or mast cells, among others, have been described to be present in human and mouse plaques. How these populations can modulate the atherogenic process is dependent on their specialized function. DCs constitute a unique population with the ability to bridge innate and adaptive immune responses, mainly by their strong capacity to present antigens bound to a major histocompatibility complex (MHC) molecule. Given their ability to polarize T cells and secrete cytokines, their role in atherosclerosis has gained attention for the development of new therapeutic approaches that could impact lesion growth. Hence, knowing the effect of a specific subset is an initial key step to evaluate its potential for clinical purposes. For example, the basic leucine zipper ATF-like 3 transcription factor (Batf3) controls the development of conventional dendritic cells type 1 (cDCs1), characterized by the expression of the surface markers CD8 and CD103. Initially, they were described to promote both T-helper 1 (Th1) and regulatory T cell (Treg) responses, known to accelerate and to protect against atherosclerosis, respectively. The first part of this thesis aimed to elucidate the potential role of Batf3-dependent DCs in atherosclerosis and concluded that even though systemic immune responses were mildly altered they do not modify the course of the disease and may not represent an attractive candidate for clinical studies. DCs also have the ability to impact lesion growth through the release of a broad range of cytokines, which can either directly impact atherosclerotic plaques by modulating resident cells, or by further polarizing T cell responses. Among others, interleukin (IL) 23, a member of the IL-12 family of cytokines, has received much attention during the past year due to its connection to autoimmunity. IL-23 is known to induce pathogenicity of Th17 cells and is responsible for the development of several autoimmune diseases including multiple sclerosis, psoriasis or rheumatoid arthritis. Interestingly, these patients often present with an accelerated course of atherosclerosis and thus, are at higher risk of developing cardiovascular events. Several epidemiological studies have pointed toward a possible connection between IL-23 and its receptor IL-23R in atherosclerosis, although their exact contribution remains to be elucidated. The second part of this thesis showed that resident antigen-presenting cells (APCs) in the aorta produced IL-23 during the steady state but this secretion was greatly enhanced after incubation with oxidized low-density lipoprotein (oxLDL). Furthermore, disruption of the IL-23R signaling led to decreased relative necrotic plaque area in lesions of Ldlr-/-Il23r-/- mice fed a high-fat diet (HFD) for 6 and 12 weeks compared to Ldlr-/- controls. A proposed mechanism involves that increased IL-23 production in the context of atherosclerosis may promote the pathogenicity of IL-23-responding T cells, especially IL-23R+ γδ T cells in the aortic root. Response to IL-23 might increase the release of granulocyte-macrophage colony-stimulating factor (GM-CSF) and IL-17 and alter the pro- and anti-inflammatory balance of cytokines in the aortic root. Altogether, these data showed that the IL-23 / IL-23R axis play a role in plaque stability.},
  subject      = {Arteriosklerose},
  language  = {en}
}
@phdthesis{Baumann2018,
  author    = {Baumann, Christian},
  title     = {Psychologische und genetische Einflussfaktoren auf die Furchtkonditionierung und die Generalisierung konditionierter Furcht},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-153656},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {Bei der Entstehung und Aufrechterhaltung von Furcht und Angsterkrankungen stellt, neben der Furchtkonditionierung, die Generalisierung der konditionierten Furcht einen wesentlichen Mechanismus dar. Die der Generalisierung zugrunde liegenden psychologischen und biologischen Prozesse sind jedoch beim Menschen bisher nur wenig untersucht. Ziel dieser Arbeit war, anhand eines neu entwickelten experimentellen Paradigmas den Einfluss eines psychometrisch bestimmbaren angstspezifischen Faktors sowie der mit Furcht und Angst assoziierten Genotypen Stathmin1, COMT Val158Met und BDNF Val66Met auf die Furchtkonditionierung und Generalisierung konditionierter Furcht zu untersuchen und somit m{\"o}gliche Risikofaktoren f{\"u}r die Entstehung von Angsterkrankungen zu bestimmen. Hierf{\"u}r wurden N = 126 gesunde Versuchspersonen (n = 69 weiblich; mittleres Alter M = 23.05, SD = 3.82) f{\"u}r die genannten Polymorphismen genotypisiert und zu {\"a}ngstlichen und affektiven Symptomen befragt. In einer Akquisitionsphase wurden den Probanden zwei neutrale weibliche Gesichter pr{\"a}sentiert (CS), von denen eines mit einem Schrei sowie einem {\"a}ngstlichen Gesichtsausdruck (UCS) gepaart wurde. Der sich anschließende Generalisierungstest erfolgte anhand von vier Gesichtern, die in der {\"A}hnlichkeit zwischen den beiden CS schrittweise {\"u}bergingen. Die Furchtreaktion wurde {\"u}ber die Bewertung von Valenz, Arousal und Kontingenzerwartung sowie {\"u}ber die Hautleitf{\"a}higkeitsreaktion (SCR) erfasst. Die Analyse der Frageb{\"o}gen anhand einer Hauptachsenanalyse und anhand von Strukturgleichungsmodellen erbrachte eine zweifaktorielle L{\"o}sung, die die Konstrukte Depression und Angst abbildete. Nur der Faktor Angst war mit einer ver{\"a}nderten Furchtkonditionierung und Furchtgeneralisierung assoziiert: Hoch {\"A}ngstliche zeigten eine st{\"a}rkere konditionierte Furchtreaktion (Arousal) und wiesen eine st{\"a}rkere Generalisierung der Valenzeinsch{\"a}tzung und Kontingenzerwartung auf. F{\"u}r den Stathmin1 Genotyp ergaben sich geschlechtsspezifische Effekte. Bei den m{\"a}nnlichen Versuchspersonen zeigte sich in Folge der Akquisition ein st{\"a}rkerer Abfall der Valenz f{\"u}r den CS+ in der Gruppe der Stathmin1 T Alleltr{\"a}ger, die ebenfalls eine st{\"a}rkere Generalisierung der Furchtreaktion, abgebildet in allen verbalen Maßen, aufwiesen. Ein gegenteiliger Befund ergab sich f{\"u}r die Gruppe der Frauen, insofern eine mit dem Stathmin1 C Allel assoziierte h{\"o}here Generalisierung der Valenz, des Arousals und der Kontingenzerwartung festgestellt werden konnte. F{\"u}r den COMT Val158Met Genotyp ergaben sich keine Einfl{\"u}sse auf die Akquisition der konditionierten Furcht. F{\"u}r Tr{\"a}ger des COMT 158Val Allels zeigte sich jedoch eine st{\"a}rkere Generalisierung der Valenz und der Kontingenzerwartung. Auch f{\"u}r den BDNF Val66Met Genotyp konnte keine Ver{\"a}nderung der Furchtakquisition beobachtet werden. Es ergaben sich jedoch Hinweise auf eine erh{\"o}hte Generalisierung der Kontingenzerwartung in der Gruppe der BDNF 66Val Homozygoten. F{\"u}r keinen der beschriebenen Faktoren konnte ein Einfluss auf die Furchtkonditionierung oder deren Generalisierung anhand der SCR abgebildet werden. Unsere Ergebnisse weisen auf einen psychometrisch erfassbaren Faktor und genetische Einfl{\"u}sse hin, die {\"u}ber den Prozess einer st{\"a}rkeren Generalisierung der konditionierten Furcht das Risiko f{\"u}r die Entstehung von Angsterkrankungen erh{\"o}hen k{\"o}nnen. Jedoch sollten die Befunde in gr{\"o}ßeren Stichproben repliziert werden. Neben der fr{\"u}hzeitigen Identifikation von Risikofaktoren sollten in zuk{\"u}nftigen Studien dar{\"u}ber hinaus wirksame Maßnahmen zur Pr{\"a}vention und Intervention entwickelt werden, um diesem Risiko entgegen zu wirken.},
  subject      = {Konditionierung},
  language  = {de}
}
@phdthesis{Uthe2018,
  author    = {Uthe, Friedrich Wilhelm},
  title     = {Identifikation synthetisch-letaler Interaktionen mit dem Tumorsuppressor APC und Beeinflussung von MYC-Proteinmengen durch Translationsinhibition im kolorektalen Karzinom},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166451},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {Der Tumorsupressor APC ist in der Mehrzahl aller F{\"a}lle kolorektaler Karzinome bereits in der initialen Phase der Karzinogenese mutiert. Diese Mutationen f{\"u}hren zu einer aberranten Aktivierung des Wnt-Signalweges sowie zu weiteren die Karzinogenese vorrantreibenden Aktivit{\"a}ten, beispielsweise einem ver{\"a}nderten Migrationsverhalten. Dieser Dissertation zu Grunde liegt die Idee, dass durch die Trunkierung des APC-Proteins aber auch Abh{\"a}ngigkeiten von Genaktivit{\"a}ten entstehen, die zuvor entbehrlich waren. Solche synthetisch letalen Gene sollten in einem high-content shRNA-Screen gefunden werden. F{\"u}r die Durchf{\"u}hrung des Screens wurde ein von der SW480 Kolonkarzinomzelllinie abgeleitetes, isogenes Zellsystem generiert, welches durch Induktion mit Doxyzyklin das vollst{\"a}ndige APC-Allel (FL-APC) exprimiert. Infolge dieser Expression zeigen die Zellen einen weniger malignen Ph{\"a}notyp. Dies spiegelt sich darin wider, dass die Zellen durch FL-APC Expression in ihrer Wnt-Signalwegsaktivit{\"a}t eingeschr{\"a}nkt werden. Doxyzyklininduzierte Zellen sind schlechter in der Lage ohne Adh{\"a}sion zu proliferieren als nicht induzierte Zellen. Andererseits ist ihre F{\"a}higkeit einem FKS-gradienten entlang zu migrieren verbessert. Der shRNA-Screen wurde mit der Decipher shRNA-Bibliothek durchgef{\"u}hrt. Diese enth{\"a}lt 27.500 verschiedene shRNAs mit Interferenzaktivit{\"a}t gegen 5.000 mRNAs, die potentiell pharmakologisch inhibierbare Proteine kodieren. Die besten zwei Kandidaten f{\"u}r eine synthetisch letale Interaktion mit trunkiertem APC, BCL2L1 und EIF2B5 wurden im Verlauf einer Masterarbeit bzw. direkt in dieser Disseration validiert. EIF2B5 zeigte in vitro nach Depletion durch unterschiedliche shRNAs einen di erentiellen Proliferationse ekt bei FL-APC induzierten im Vergleich zu kontrollbehandelten Zellen. Dieser di erentielle E ekt konnte in einem weiteren Modellsystem, SW480 Zellen mit konstitutiver FL-APC Expression, ebenfalls validiert werden. Durch Expression einer shRNA mit Aktivit{\"a}t gegen EIF2B5 werden in beiden Zellsystem die unfolded protein response (UPR) Gene DDIT3 und splXBP1 aktiviert. Interessanterweise werden durch die Expression von FL-APC diese Gene reprimiert. Im Promotor der EIF2B5-mRNA be ndet sich eine Bindestelle f{\"u}r MYC. Es ist denkbar, dass durch die Expression von FL-APC eine globale Ver{\"a}nderung der Genexpression vorgenommen wird, die einerseits eine Repression von EIF2B5 nach sich zieht aber andererseits eine hierdurch ausgel{\"o}ste ER-Stress Antwort verhindert. Eine Inhibition von EIF2B5 ohne diese Adaption andererseits f{\"u}hrt nach diesem Model zu einer UPR-aktivierten Apoptose. In einem zweiten Projekt wurde das {\"u}berraschende Verhalten von Kolonkarzinomzellen untersucht, die nach Zugabe von BEZ235, einem dualen PI3K/mTOR Inhibitor, trotz gegenteiliger Erwartungen MYC-Proteinmengen erh{\"o}hen. Eine Repression wurde erwar- tet, weil die Inhibition von PI3K einerseits zu einer proteasomalen Destabiliserung und andererseits die mTOR Inhibition zu einer verringerten Synthese von MYC f{\"u}hren sollte. W{\"a}hrend bereits gezeigt werden konnte, dass durch einen FOXO-vermittelten Mechanismus MAPK-abh{\"a}ngig die MYC-Expression verst{\"a}rkt wird, wurde in dieser Dissertation die erwartete Translationsinhibition untersucht. BEZ235 inhibiert zwar CAP-abh{\"a}ngige Translation, das MYC Protein wird jedoch aufgrund einer IRES-vermittelten Translation weiterhin exprimiert. Silvestrol, ein Inhibitor der Helikase eIF4A andererseits interveniert mit CAP- und IRES-abh{\"a}ngiger Translation und kann die MYC-Proteinkonzentrationen verringern. Wir konnten zudem feststellen, dass die Applikation von Silvestrol auch in vivo m{\"o}glich und wirksam ist und zudem tolleriert wird. Dies gibt Anlass zur Ho nung, dass eine Intervention der Translation auch im Menschen eine valide Strategie zur Behandlung MYC-getriebener Tumore sein k{\"o}nnte.},
  subject      = {Colonkrebs},
  language  = {de}
}
@phdthesis{TawkTaouk2018,
  author    = {Tawk [Taouk], Caroline S.},
  title     = {The role of host-stress in the infection by the bacterial pathogen \(Shigella\) \(flexneri\)},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-151107},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {The human-bacterial pathogen interaction is a complex process that results from a prolonged evolutionary arms race in the struggle for survival. The pathogen employs virulence strategies to achieve host colonization, and the latter counteracts using defense programs. The encounter of both organisms results in drastic physiological changes leading to stress, which is an ancient response accompanying infection. Recent evidence suggests that the stress response in the host converges with the innate immune pathways and influences the outcome of infection. However, the contribution of stress and the exact mechanism(s) of its involvement in host defense remain to be elucidated. Using the model bacterial pathogen Shigella flexneri, and comparing it with the closely related pathogen Salmonella Typhimurium, this study investigated the role of host stress in the outcome of infection. Shigella infection is characterized by a pronounced pro-inflammatory response that causes intense stress in host tissues, particularly the intestinal epithelium, which constitutes the first barrier against Shigella colonization. In this study, inflammatory stress was simulated in epithelial cells by inducing oxidative stress, hypoxia, and cytokine stimulation. Shigella infection of epithelial cells exposed to such stresses was strongly inhibited at the adhesion/binding stage. This resulted from the depletion of sphingolipidrafts in the plasma membrane by the stress-activated sphingomyelinases. Interestingly, Salmonella adhesion was not affected, by virtue of its flagellar motility, which allowed the gathering of bacteria at remaining membrane rafts. Moreover, the intracellular replication of Shigella lead to a similar sphingolipid-raft depletion in the membrane across adjacent cells inhibiting extracellular bacterial invasion. Additionally, this study shows that Shigella infection interferes with the host stress granule-formation in response to stress. Interestingly, infected cells exhibited a nuclear depletion of the global RNA-binding stress-granule associated proteins TIAR and TIA-1 and their accumulation in the cytoplasm. Overall, this work investigated different aspects of the host stress-response in the defense against bacterial infection. The findings shed light on the importance of the host stress-pathways during infection, and improve the understanding of different strategies in host-pathogen interaction.},
  subject      = {Shigella flexneri},
  language  = {en}
}
@phdthesis{Glueck2018,
  author    = {Gl{\"u}ck, Lucia},
  title     = {Aktivierung des MEK5/ Erk5-Signalwegs durch inhibitorische Substanzen des Mevalonatstoffwechsels},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-162084},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {Die Osteoporose ist eine Erkrankung, die durch verminderte Dichte und erh{\"o}hte Fragilit{\"a}t des Knochens gekennzeichnet ist. Sie z{\"a}hlt zu den h{\"a}ufigsten Erkrankungen weltweit und geht mit erheblicher Einschr{\"a}nkung der Lebensqualit{\"a}t und erh{\"o}hter Mortalit{\"a}t einher. Eine Behandlungsm{\"o}glichkeit dieses schwerwiegenden Krankheitsbilds ist die Therapie mit Bisphosphonaten. Diese hemmen mit ihren antiresorptiven Eigenschaften den Knochenabbau und f{\"o}rdern vermutlich gleichzeitig den Knochenaufbau. Obwohl schon lange die Wirkungsweise der Bisphosphonate erforscht wird, ist noch nicht sicher gekl{\"a}rt, wie beispielsweise osteoanabole oder antitumor{\"o}se Effekte vermittelt werden. Einen Erkl{\"a}rungsansatz bietet der MEK5/ Erk5-Signalweg. Diesem werden unter anderem antiangiogenetische, antiinflammatorische und antiproliferative Eigenschaften zugesprochen. In fr{\"u}heren Studien konnte gezeigt werden, dass Statine Erk5 und Erk5-abh{\"a}ngige Gene aktivieren k{\"o}nnen. Statine wiederum inhibieren ebenfalls den Mevalonatstoffwechsel, jedoch weiter upstream als Bisphosphonate. Da Statine zudem osteoanabole Effekte aufweisen, lag die These nahe, dass auch Bisphosphonate ihre Wirkung {\"u}ber den MEK5/Erk5-Signalweg vermitteln k{\"o}nnten. Die These konnte im Rahmen dieser Arbeit best{\"a}tigt werden: Stickstoffhaltige, nicht aber stickstofffreie Bisphosphonate aktivieren Erk5 sowohl in Endothelzellen als auch in Osteoblasten. Es gilt jedoch zu bedenken, dass eine Weiterentwicklung der Substanzen mit verbesserter Aufnahme in die Zelle zur Vermeidung von Apoptose-Induktion anzustreben ist. Des Weiteren konnte gezeigt werden, dass ein Knock-down der FDPS, dem Angriffspunkt der Bisphosphonate im Mevalonatstoffwechsel, ebenfalls eine Erk5-Phosphorylierung zur Folge hat. Durch Inhibition der FDPS wird die Prenylierung kleiner G-Proteine wie Cdc42 unterbunden, was eine ver{\"a}nderte Funktion der Proteine zur Folge hat. Ein Knock-down von Cdc42 mittels siRNA f{\"u}hrt wiederum zu einer Aktivierung von Erk5. Auf diese Weise wurde nicht nur ein neuer Wirkungsweg der Bisphosphonate identifiziert, sondern auch ein m{\"o}glicher Aktivierungsmechanismus der MEK5/ Erk5-Signalkaskade aufgedeckt. Erk5 wandert nach seiner Aktivierung in den Zellkern und beeinflusst dort die Genexpression. Im Rahmen dieser Arbeit wurden knochenrelevante Gene identifiziert, die durch Zoledronat-Stimulation induziert werden konnten. Zu diesen z{\"a}hlen INPP4B, das die Osteoklastogenese inhibiert, und PTHLH sowie FOSL1, welche die Osteoblastogenese f{\"o}rdern. Somit kann davon ausgegangen werden, dass die Aktivierung des MEK5/ Erk5-Signalwegs durch Zoledronat eine Geninduktion zur Folge hat, die sowohl die osteoanabole Wirkung unterst{\"u}tzt, als auch die katabolen Effekte hemmt. Auf diese Weise konnte neben den bereits bekannten Wirkungswegen der Bisphosphonate ein neuer identifiziert werden, der auch einen m{\"o}glichen Ansatz f{\"u}r weitere, bisher ungekl{\"a}rte Effekte von Bisphosphonaten darstellt.},
  subject      = {Bisphosphonate},
  language  = {de}
}
@phdthesis{Raab2018,
  author    = {Raab, Annette},
  title     = {The role of Rgs2 in animal models of affective disorders},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-152550},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {Anxiety and depressive disorders result from a complex interplay of genetic and environmental factors and are common mutual comorbidities. On the level of cellular signaling, regulator of G protein signaling 2 (Rgs2) has been implicated in human and rodent anxiety as well as rodent depression. Rgs2 negatively regulates G protein-coupled receptor (GPCR) signaling by acting as a GTPase accelerating protein towards the Gα subunit. The present study investigates, whether mice with a homozygous Rgs2 deletion (Rgs2-/-) show behavioral alterations as well as an increased susceptibility to stressful life events related to human anxiety and depressive disorders and tries to elucidate molecular underlying's of these changes. To this end, Rgs2-/- mice were characterized in an aversive-associative learning paradigm to evaluate learned fear as a model for the etiology of human anxiety disorders. Spatial learning and reward motivated spatial learning were evaluated to control for learning in non-aversive paradigms. Rgs2 deletion enhanced learning in all three paradigms, rendering increased learning upon deletion of Rgs2 not specific for aversive learning. These data support reports indicating increased long-term potentiation in Rgs2-/- mice and may predict treatment response to conditioning based behavior therapy in patients with polymorphisms associated with reduced RGS2 expression. Previous reports of increased innate anxiety were corroborated in three tests based on the approach-avoidance conflict. Interestingly, Rgs2-/- mice showed novelty-induced hypo-locomotion suggesting neophobia, which may translate to the clinical picture of agoraphobia in humans and reduced RGS2 expression in humans was associated with a higher incidence of panic disorder with agoraphobia. Depression-like behavior was more distinctive in female Rgs2-/- mice. Stress resilience, tested in an acute and a chronic stress paradigm, was also more distinctive in female Rgs2-/- mice, suggesting Rgs2 to contribute to sex specific effects of anxiety disorders and depression. Rgs2 deletion was associated with GPCR expression changes of the adrenergic, serotonergic, dopaminergic and neuropeptide Y systems in the brain and heart as well as reduced monoaminergic neurotransmitter levels. Furthermore, the expression of two stress-related microRNAs was increased upon Rgs2 deletion. The aversive-associative learning paradigm induced a dynamic Rgs2 expression change. The observed molecular changes may contribute to the anxious and depressed phenotype as well as promote altered stress reactivity, while reflecting an alter basal stress level and a disrupted sympathetic tone. Dynamic Rgs2 expression may mediate changes in GPCR signaling duration during memory formation. Taken together, Rgs2 deletion promotes increased anxiety-like and depression-like behavior, altered stress reactivity as well as increased cognitive function.},
  subject      = {Angst},
  language  = {en}
}
@phdthesis{Huang2018,
  author    = {Huang, Hua},
  title     = {Comparative investigation of the chemical composition and the water permeability of fruit and leaf cuticles},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-152948},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {The plant cuticle is a continuous extracellular protective layer covering the outermost surfaces of higher plants that are in contact with the surrounding atmosphere. The primary function of the cuticular lipid membrane, which is mainly composed of biopolymer cutin and cuticular waxes, is to protect the plant organs against uncontrolled water loss. The chemical composition and the biophysical properties of cuticular waxes affect the rate of water diffusion across the cuticle. Fruit transpiration plays an important role in the development and the maintenance of fruit quality. The fruit has been suggested to present better dehydration stress tolerance than the leaf. However, the differences in transpiration and the chemical composition of cuticular waxes between fruit and leaf have yet to be comprehensively investigated. The present study aims to investigate the water permeability and cuticular wax composition of fruit and leaf cuticles of a wide range of plant species and to elucidate the different roles of the cuticular wax components in the transpiration barrier. To address these objectives, fruit and leaf samples from 17 species were investigated. The cuticular transpiration of intact fruits and astomatous adaxial leaf surfaces and the minimum leaf conductance obtained by leaf drying curves for intact leaves were gravimetrically determined for a variety of plant species. The chemical composition of cuticular waxes of fruits and leaves was thoroughly analysed by gas chromatography with flame ionization and mass spectrometry. The water permeability of fruits ranged from 3.7 x 10-5 m s-1 (Prunus domestica subsp. syriaca) to 37.4 x 10-5 m s-1 (Coffea arabica), whereas permeability for leaves varied between 1.6 x 10-5 m s-1 (Cornus officinalis) and 4.5 x 10-5 m s-1 (Prunus domestica subsp. syriaca (L.)). The interspecies range of water permeability of fruits was significantly higher than that of leaves. Chemical analyses of the cuticular waxes demonstrated that fatty acids, primary alcohols, n-alkanes, aldehydes and alkyl esters were the predominant very-long-chain aliphatic compound classes of fruit and leaf surfaces. Sterols, such as β-sitosterol and campesterol, and triterpenoids, such as oleanolic acid, ursolic acid, α-amyrin and ß-amyrin, were the major cyclic compound classes in the cuticular wax membrane. The amount and composition of cuticular waxes of both fruits and leaves varied at an intraspecific level. There were no significant correlations between the total cuticular wax load or the individual cuticular wax composition and the water permeability of fruits or leaves independently or together. After combining the fruit and leaf data set, a significant correlation between the average chain length of very-long-chain aliphatic compounds and permeabilities was detected, i.e. the longer the average chain length, the lower the water permeability. Interestingly, n-Nonacosane (C29) was abundantly detected in fruit waxes of Rosaceae species. These fruits exhibited a relatively low transpiration level, which was very close to their leaf cuticular permeability. The present study suggests that the lower cuticular permeability of leaves, in comparison to that of fruits, may be attributed to the longer average chain length of aliphatic compounds. The accumulation of total wax, triterpenoids and aliphatic compounds may not contribute to the transpiration barrier directly. The present results are highly consistent with the previous model assumptions for the cuticular structure and transport barrier. Furthermore, this comparative study on leaf and fruit cuticles provides further insights linking the cuticular wax chemistry to the physiological properties of the plant cuticle.},
  subject      = {Cuticle},
  language  = {en}
}
@phdthesis{Schedler2018,
  author    = {Schedler, Anette},
  title     = {Analyse von Wirt-Pathogen-Interaktionen zur Untersuchung des Einflusses von \(Aspergillus\) \(fumigatus\) auf die H{\"a}mostase},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-152512},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {Als H{\"a}mostase bezeichnet man die Gesamtheit der Reaktionen, die zu einer effektiven Blutgerinnung beitragen. Sie l{\"a}sst sich in die prim{\"a}re (thrombozyt{\"a}re) H{\"a}mostase, in die sekund{\"a}re (plasmatische) H{\"a}mostase und in das Fibrinolysesystem einteilen. Thrombozyten, oder auch Pl{\"a}ttchen genannt, spielen hierbei eine entscheidende Rolle. Sie binden an die durch eine Verletzung einer Blutgef{\"a}ßwand freigelegten Faktoren, werden so aktiviert und aggregieren mit weiteren Thrombozyten, wodurch ein Thrombus entsteht, der die Verletzung verschließt. Zudem besitzen Thrombozyten Immunokompetenz und k{\"o}nnen mit anderen Immunzellen interagieren, {\"u}ber Rezeptoren Pathogene erkennen und sie direkt angreifen. Einer dieser Pathogene ist der opportunistische Pilz Aspergillus fumigatus. Dieser bildet im Verlauf seines Lebenszyklus 2,5 -3 µm kleine Konidien aus, die mit dem Wind verbreitet werden und bis tief in die Alveolen der menschlichen Lunge eingeatmet werden k{\"o}nnen. W{\"a}hrend diese Konidien im gesunden Menschen durch das Immunsystem und andere Abwehrmechanismen eliminiert werden, k{\"o}nnen sie im immunsupprimierten Patienten, z. B. bei Patienten nach einer h{\"a}matopoietischen Stammzelltransplantation, auskeimen und verschiedene Krankheiten, sogenannte Aspergillosen, ausl{\"o}sen mit der Invasiven Aspergillose (IA) als schwerwiegendste Form. Diese ist assoziiert mit Gewebezerst{\"o}rungen, Blutungen und Thrombenbildung am Ort der Infektion. Diese Komplikationen k{\"o}nnten auf einer {\"u}berh{\"o}hten Immunantwort des Wirtes, auf dem mechanischen Eindringen des Pilzes in das Gewebe und die Blutgef{\"a}ße oder auf einer {\"A}nderung der lokalen H{\"a}mostase durch sezernierte hydrolytische Enzyme (Proteasen) oder Sekund{\"a}rmetabolite von A. fumigatus beruhen. Um diese {\"A}nderung der H{\"a}mostase im Verlauf einer IA zu analysieren, wurde der Einfluss von Morphologien (Konidien, geschwollene Konidien, Keimschl{\"a}uche und Hyphen), deren {\"U}berst{\"a}nde, sowie von proteolytisch aktivem {\"U}berstand und von verschiedenen Sekund{\"a}rmetaboliten von A. fumigatus auf die sekund{\"a}re H{\"a}mostase und die Aggregation und Aktivit{\"a}t von humanen Thrombozyten untersucht. Bei der Analyse der sekund{\"a}ren H{\"a}mostase konnte f{\"u}r keinen dieser eingesetzten Effektoren ein Einfluss festgestellt werden. Bei der Analyse der prim{\"a}ren H{\"a}mostase und dem Einsatz von Morphologien und ihrer {\"U}berst{\"a}nde konnte f{\"u}r Hyphen und ihren ankonzentrierten {\"U}berstand eine aggregationssteigernde Wirkung auf Thrombozyten beobachtet werden, die m{\"o}glicherweise auf Bestandteile der Zellwand von A. fumigatus, wie z. B. β-Galactosaminogalactan (GAG) zur{\"u}ckzuf{\"u}hren ist. Proteolytisch aktiver {\"U}berstand f{\"u}hrte zu einer Aktivierung der Thrombozyten, die zum Teil auf die PrtT-abh{\"a}ngige proteolytische Spaltung und damit die Aktivierung der Thrombinrezeptoren PAR1 und/oder PAR4 auf der Thrombozytenoberfl{\"a}che, zum Teil aber auch auf GAG zur{\"u}ckzuf{\"u}hren sein kann. Von den hier verwendeten Mykotoxinen Gliotoxin, Fumagillin, Citrinin, Verruculogen und Deoxynivalenol konnte f{\"u}r Gliotoxin ein negativer Einfluss auf die Thrombozytenaktivit{\"a}t nachgewiesen werden. Dieses Toxin inhibierte die Aggregation und die Aktivit{\"a}t der Thrombozyten, m{\"o}glicherweise durch die Bildung von Disulfid-Br{\"u}ckenbindungen oder auch durch die Bildung von reaktiven Sauerstoffspezies. Zudem wurde im Verlauf dieser Arbeit eine direkte Interaktion von Gliotoxin mit den ADP-Rezeptoren P2Y1 und P2Y12 sowie mit dem Integrin αIIbβ3 postuliert, die so zwar nicht best{\"a}tigt, aber auch nicht vollst{\"a}ndig wiederlegt werden konnte. Die hier dargestellten Ergebnisse zeigen deutlich zwei Wirkungen von A. fumigatus auf humane Thrombozyten: zum einen eine Aktivierung oder auch verst{\"a}rkte Aggregation durch sezernierte Proteasen oder Zellwandbestandteile, zum anderen eine Hemmung durch Gliotoxin, was die bei einer IA beobachtete Thrombenbildung sowie die Blutungen erkl{\"a}ren kann. Die Interaktion der aktivierten Thrombozyten mit den Zellen des Immunsystems sowie die zytotoxischen Eigenschaften von Gliotoxin k{\"o}nnten zudem f{\"u}r die beobachtete Gewebezerst{\"o}rung verantwortlich sein. Dennoch ist weitere Forschung in diesem Gebiet unabdingbar, um die pathophysiologische {\"A}nderung der lokalen H{\"a}mostase durch A. fumigatus und seine Wirkung auf humane Thrombozyten besser zu verstehen und so eine schnellere Erkennung und Behandlung von Aspergillosen zu erm{\"o}glichen.},
  subject      = {Aspergillus fumigatus},
  language  = {de}
}
@phdthesis{Kauk2018,
  author    = {Kauk, Michael},
  title     = {Investigating the Molecular Mechanism of Receptor Activation at Muscarinic Receptors by Means of Pathway-Specific Dualsteric Ligands and Partial Agonists},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-173729},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {G protein-coupled receptors (GPCRs) form the biggest receptor family that is encoded in the human genome and represent the most druggable target structure for modern therapeutics respectively future drug development. Belonging to aminergic class A GPCRs muscarinic Acetylcholine receptors (mAChRs) are already now of clinical relevance and are also seen as promising future drug targets for treating neurodegenerative diseases like Alzheimer or Parkinson. The mAChR family consist of five subtypes showing high sequence identity for the endogenous ligand binding region and thus it is challenging until now to selectively activate a single receptor subtype. A well accepted method to study ligand binding, dynamic receptor activation and downstream signaling is the fluorescence resonance energy transfer (FRET) application. Here, there relative distance between two fluorophores in close proximity (<10 nm) can be monitored in a dynamic manner. The perquisite for that is the spectral overlap of the emission spectrum of the first fluorophore with the excitation spectrum of the second fluorophore. By inserting two fluorophores into the molecular receptor structure receptor FRET sensors can serve as a powerful tool to study dynamic receptor pharmacology. Dualsteric Ligands consist of two different pharmacophoric entities and are regarded as a promising ligand design for future drug development. The orthosteric part interacts with high affinity with the endogenous ligand binding region whereas the allosteric part binds to a different receptor region mostly located in the extracellular vestibule. Both moieties are covalently linked. Dualsteric ligands exhibit a dynamic ligand binding. The dualsteric binding position is characterized by a simultaneous binding of the orthosteric and allosteric moiety to the receptor and thus by receptor activation. In the purely allosteric binding position no receptor activation can be monitored. In the present work the first receptor FRET sensor for the muscarinic subtype 1 (M1) was generated and characterized. The M1-I3N-CFP sensor showed an unaltered physiological behavior as well as ligand and concentration dependent responses. The sensor was used to characterize different sets of dualsteric ligands concerning their pharmacological properties like receptor activation. It was shown that the hybrids consisting of the synthetic full agonist iperoxo and the positive allosteric modulator of BQCA type is very promising. Furthermore, it was shown for orthosteric as well as dualsteric ligands that the degree of receptor activation is highly dependent on the length of and the chemical properties of the linker moiety. For dualsteric ligands a bell-shaped activation characteristic was reported for the first time, suggesting that there is an optimal linker length for dualsteric ligands. The gained knowledge about hybrid design was then used to generate and characterize the first photo-switchable dualsteric ligand. The resulting hybrids were characterized with the M1-I3N-CFP sensor and were described as photo-inactivatable and dimmable. In addition to the ligand characterization the ligand application methodology was further developed and improved. Thus, a fragment-based screening approach for dualsteric ligands was reported in this study for the first time. With this approach it is possible to investigate dualsteric ligands in greater detail by applying either single ligand fragments alone or in a mixture of building blocks. These studies revealed the insights that the effect of dualsteric ligands on a GPCR can be rebuild by applying the single building blocks simultaneously. The fragment-based screening provides high potential for the molecular understanding of dualsteric ligands and for future screening approaches. Next, a further development of the standard procedure for measuring FRET by sensitized emission was performed. Under normal conditions single cell FRET is measured on glass coverslips. After coating the coverslips surface with a 20 nm thick gold layer an increased FRET efficiency up to 60 \% could be reported. This finding was validated in different approaches und in different configurations. This FRET enhancement by plasmonic surfaces was until yet unreported in the literature for physiological systems and make FRET for future projects even more powerful.},
  subject      = {G-Protein gekoppelte Rezeptoren},
  language  = {en}
}
@phdthesis{Bemm2018,
  author    = {Bemm, Felix Mathias},
  title     = {Genetic foundation of unrivaled survival strategies - Of water bears and carnivorous plants -},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-157109},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {All living organisms leverage mechanisms and response systems to optimize reproduction, defense, survival, and competitiveness within their natural habitat. Evolutionary theories such as the universal adaptive strategy theory (UAST) developed by John Philip Grime (1979) attempt to describe how these systems are limited by the trade-off between growth, maintenance and regeneration; known as the universal three-way trade-off. Grime introduced three adaptive strategies that enable organisms to coop with either high or low intensities of stress (e.g., nutrient deficiency) and environmental disturbance (e.g., seasons). The competitor is able to outcompete other organisms by efficiently tapping available resources in environments of low intensity stress and disturbance (e.g., rapid growers). A ruderal specism is able to rapidly complete the life cycle especially during high intensity disturbance and low intensity stress (e.g., annual colonizers). The stress tolerator is able to respond to high intensity stress with physiological variability but is limited to low intensity disturbance environments. Carnivorous plants like D. muscipula and tardigrades like M. tardigradum are two extreme examples for such stress tolerators. D. muscipula traps insects in its native habitat (green swamps in North and South Carolina) with specialized leaves and thereby is able to tolerate nutrient deficient soils. M. tardigradum on the other side, is able to escape desiccation of its terrestrial habitat like mosses and lichens which are usually covered by a water film but regularly fall completely dry. The stress tolerance of the two species is the central study object of this thesis. In both cases, high througput sequencing data and methods were used to test for transcriptomic (D. muscipula) or genomic adaptations (M. tardigradum) which underly the stress tolerance. A new hardware resource including computing cluster and high availability storage system was implemented in the first months of the thesis work to effectively analyze the vast amounts of data generated for both projects. Side-by-side, the data management resource TBro [14] was established together with students to intuitively approach complex biological questions and enhance collaboration between researchers of several different disciplines. Thereafter, the unique trapping abilities of D. muscipula were studied using a whole transcriptome approach. Prey-dependent changes of the transcriptional landscape as well as individual tissue-specific aspects of the whole plant were studied. The analysis revealed that non-stimulated traps of D. muscipula exhibit the expected hallmarks of any typical leaf but operates evolutionary conserved stress-related pathways including defense-associated responses when digesting prey. An integrative approach, combining proteome and transcriptome data further enabled the detailed description of the digestive cocktail and the potential nutrient uptake machinery of the plant. The published work [25] as well as a accompanying video material (https://www.eurekalert.org/pub_releases/ 2016-05/cshl-fgr042816.php; Video credit: S{\"o}nke Scherzer) gained global press coverage and successfully underlined the advantages of D. muscipula as experimental system to understand the carnivorous syndrome. The analysis of the peculiar stress tolerance of M. tardigradum during cryptobiosis was carried out using a genomic approach. First, the genome size of M. tardigradum was estimated, the genome sequenced, assembled and annotated. The first draft of M. tardigradum and the workflow used to established its genome draft helped scrutinizing the first ever released tardigrade genome (Hypsibius dujardini) and demonstrated how (bacterial) contamination can influence whole genome analysis efforts [27]. Finally, the M. tardigradum genome was compared to two other tardigrades and all species present in the current release of the Ensembl Metazoa database. The analysis revealed that tardigrade genomes are not that different from those of other Ecdysozoa. The availability of the three genomes allowed the delineation of their phylogenetic position within the Ecdysozoa and placed them as sister taxa to the nematodes. Thereby, the comparative analysis helped to identify evolutionary trends within this metazoan lineage. Surprisingly, the analysis did not reveal general mechanisms (shared by all available tardigrade genomes) behind the arguably most peculiar feature of tardigrades; their enormous stress tolerance. The lack of molecular evidence for individual tardigrade species (e.g., gene expression data for M. tardigradum) and the non-existence of a universal experimental framework which enables hypothesis testing withing the whole phylum Tardigrada, made it nearly impossible to link footprints of genomic adaptations to the unusual physiological capabilities. Nevertheless, the (comparative) genomic framework established during this project will help to understand how evolution tinkered, rewired and modified existing molecular systems to shape the remarkable phenotypic features of tardigrades.},
  subject      = {B{\"a}rtierchen},
  language  = {en}
}
@phdthesis{Uthe2018,
  author    = {Uthe, Henriette},
  title     = {Analyse des Interaktoms des Mediatorkomplexes und seiner posttranslationalen Modifikationen in \(Saccharomyces\) \(Cerevisae\) mittels Massenspektrometrie},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-162619},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {Eukaryotic messenger RNA (mRNA) synthesis catalyzed by the RNA Polymerase II is the central and critical process for the regulation of gene expression. Several decades of research unearthed many details about this essential process of high complexity and dynamic. The mediator complex turned out to be crucial for the regulation of Pol II mediated transcription, especially the process of initiation. It functions as an interface between the general transcription machinery and multiple DNA binding transcriptional regulators. Binding these regulators via its tail module and binding the polymerase II via its head module, the mediator forms a bridge between upstream activating sequences and the core promotor and initiates the assembling of the Pre-Initiation complex consisting of the polymerase II and the general transcription factors. However, particularly the last years of research suggest the mediator complex within many other functions including transcription elongation, gene looping and chromatin remodeling. Considering the facts, that the mediator (a) consist of 25 subunits, which are partially flexible associated, (b) shows a flexible intrinsic structure and (c) is highly and dynamically phosphorylated it becomes easy to imagineplausible that the mediator complex meets all this functions, by serving as a transcriptional platform. In context of this thesis, and it was possible to "illustrate" the mediator within its versatile tasks and functions by presenting the most comprehensive analysis of the Mediator complex interactome to date. By optimizing the conditions of cell lysis and co-immunoprecipitation it was possible to preserve even transient and labile protein-protein interactions. The use of metabolic labeling (15N) in the control experiment, allowed us to distinguish between specific and non-specific captured proteins. In combination with high performance mass spectrometry, more than 400 proteins and even complete protein complexes interacting with the mediator complex could be identified, naming RNA-Polymerase II, all general transcription factors the SAGA complex, chromatin remodeling complexes and highly acetylated histones. Furthermore, many candidates where identified playing a role in co-transcriptional processes of mRNA, such as splicing, mRNA-decapping, mRNA transport and decay. This analysis not only confirmed several interactions , already can be found in the literature, but furthermore provide clear evidence, that mediator complex interacts not only with the RNA-Polymerase II, but also with the RNA Polymerase I and III. Next to the high numbers of potential known and unknown interacting proteins, it could be shown, that the interactome is highly dynamic and sensitive to detergent.},
  subject      = {Mediator Komplex},
  language  = {de}
}
@phdthesis{Bischler2018,
  author    = {Bischler, Thorsten David},
  title     = {Data mining and software development for RNA-seq-based approaches in bacteria},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166108},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {RNA sequencing (RNA-seq) has in recent years become the preferred method for gene expression analysis and whole transcriptome annotation. While initial RNA-seq experiments focused on eukaryotic messenger RNAs (mRNAs), which can be purified from the cellular ribonucleic acid (RNA) pool with relative ease, more advanced protocols had to be developed for sequencing of microbial transcriptomes. The resulting RNA-seq data revealed an unexpected complexity of bacterial transcriptomes and the requirement for specific analysis methods, which in many cases is not covered by tools developed for processing of eukaryotic data. The aim of this thesis was the development and application of specific data analysis methods for different RNA-seq-based approaches used to gain insights into transcription and gene regulatory processes in prokaryotes. The differential RNA sequencing (dRNA-seq) approach allows for transcriptional start site (TSS) annotation by differentiating between primary transcripts with a 5'-triphosphate (5'-PPP) and processed transcripts with a 5'-monophosphate (5'-P). This method was applied in combination with an automated TSS annotation tool to generate global trancriptome maps for Escherichia coli (E. coli) and Helicobacter pylori (H. pylori). In the E. coli study we conducted different downstream analyses to gain a deeper understanding of the nature and properties of transcripts in our TSS map. Here, we focused especially on putative antisense RNAs (asRNAs), an RNA class transcribed from the opposite strand of known protein-coding genes with the potential to regulate corresponding sense transcripts. Besides providing a set of putative asRNAs and experimental validation of candidates via Northern analysis, we analyzed and discussed different sources of variation in RNA-seq data. The aim of the H. pylori study was to provide a detailed description of the dRNA-seq approach and its application to a bacterial model organism. It includes information on experimental protocols and requirements for data analysis to generate a genome-wide TSS map. We show how the included TSS can be used to identify and analyze transcriptome and regulatory features and discuss challenges in terms oflibrary preparation protocols, sequencing platforms, and data analysis including manual and automated TSS annotation. The TSS maps and associated transcriptome data from both H. pylori and E. coli were made available for visualization in an easily accessible online browser. Furthermore, a modified version of dRNA-seq was used to identify transcriptome targets of the RNA pyrophosphohydrolase (RppH) in H. pylori. RppH initiates 5'-end-dependent degradation of transcripts by converting the 5'-PPP of primary transcripts to a 5'-P. I developed an analysis method, which uses data from complementary DNA (cDNA) libraries specific for transcripts carrying a 5'-PPP, 5'-P or both, to specifically identify transcripts modified by RppH. For this, the method assessed the 5'-phosphorylation state and cellular concentration of transcripts in rppH deletion in comparison to strains with the intact gene. Several of the identified potential RppH targets were further validated via half-life measurements and quantification of their 5'-phosphorylation state in wild-type and mutant cells. Our findings suggest an important role for RppH in post-transcriptional gene regulationin H. pylori and related organisms. In addition, we applied two RNA-seq -based approaches, RNA immunoprecipitation followed by sequencing (RIP-seq) and cross-linking immunoprecipitation followed by sequencing (CLIP-seq), to identify transcripts bound by Hfq and CsrA, two RNA-binding proteins (RBPs) with an important role in post-transcriptional regulation. For RIP-seq -based identification of CsrA binding regions in Campylobacter jejuni(C. jejuni), we used annotation-based analysis and, in addition, a self-developed peak calling method based on a sliding window approach. Both methods revealed flaA mRNA, encoding the major flagellin, as the main target and functional analysis of identified targets showed a significant enrichment of genes involved in flagella biosynthesis. Further experimental analysis revealed the role of flaA mRNA in post-transcriptional regulation. In comparison to RIP-seq, CLIP-seq allows mapping of RBP binding sites with a higher resolution. To identify these sites an approach called "block-based peak calling" was developed and resulting peaks were used to identify sequence and structural constraints required for interaction of Hfq and CsrA with Salmonella transcripts. Overall, the different RNA-seq-based approaches described in this thesis together with their associated analyis pipelines extended our knowledge on the transcriptional repertoire and modes of post-transcriptional regulation in bacteria. The global TSS maps, including further characterized asRNA candidates, putative RppH targets, and identified RBP interactomes will likely trigger similar global studies in the same or different organisms or will be used as a resource for closer examination of these features.},
  subject      = {Bakterien},
  language  = {en}
}
@article{RossowVeitlVorlovaetal.2018,
  author    = {Rossow, Leonie and Veitl, Simona and Vorlov{\´a}, Sandra and Wax, Jacqueline K. and Kuhn, Anja E. and Maltzahn, Verena and Upcin, Berin and Karl, Franziska and Hoffmann, Helene and G{\"a}tzner, Sabine and Kallius, Matthias and Nandigama, Rajender and Scheld, Daniela and Irmak, Ster and Herterich, Sabine and Zernecke, Alma and Erg{\"u}n, S{\"u}leyman and Henke, Erik},
  title     = {LOX-catalyzed collagen stabilization is a proximal cause for intrinsic resistance to chemotherapy},
  series = {Oncogene},
  volume    = {37},
  journal   = {Oncogene},
  doi       = {10.1038/s41388-018-0320-2},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-227008},
  pages     = {4921-4940},
  year      = {2018},
  abstract  = {The potential of altering the tumor ECM to improve drug response remains fairly unexplored. To identify targets for modification of the ECM aiming to improve drug response and overcome resistance, we analyzed expression data sets from pre-treatment patient cohorts. Cross-evaluation identified a subset of chemoresistant tumors characterized by increased expression of collagens and collagen-stabilizing enzymes. We demonstrate that strong collagen expression and stabilization sets off a vicious circle of self-propagating hypoxia, malignant signaling, and aberrant angiogenesis that can be broken by an appropriate auxiliary intervention: Interfering with collagen stabilization by inhibition of lysyl oxidases significantly enhanced response to chemotherapy in various tumor models, even in metastatic disease. Inhibition of collagen stabilization by itself can reduce or enhance tumor growth depending on the tumor type. The mechanistical basis for this behavior is the dependence of the individual tumor on nutritional supply on one hand and on high tissue stiffness for FAK signaling on the other.},
  language  = {en}
}
@article{JarickMokhtariSchelleretal.2018,
  author    = {Jarick, Katja J. and Mokhtari, Zeinab and Scheller, Lukas and Hartweg, Julia and Thusek, Sina and Le, Duc-Dung and Ranecky, Maria and Shaikh, Haroon and Qureischi, Musga and Heinze, Katrin G. and Beilhack, Andreas},
  title     = {Photoconversion of Alloreactive T Cells in Murine Peyer's Patches During Acute Graft-Versus-Host Disease: Tracking the Homing Route of Highly Proliferative Cells In Vivo},
  series = {Frontiers in Immunology},
  volume    = {9},
  journal   = {Frontiers in Immunology},
  doi       = {10.3389/fimmu.2018.01468},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-323309},
  year      = {2018},
  abstract  = {The regulation of immune cell migration throughout the body is essential to warrant immunosurveillance and to maintain immune homeostasis. Marking and tracking of these cells has proven important to study mechanisms of immune cell trafficking and cell interaction in vivo. Photoconversion is a well-suited technique for intravital application because it enables contactless time- and location-specific marking of cells in the tissue without surgically manipulating the microenvironment of the cells in question. However, in dividing cells the converted fluorescent protein may decline quickly. Here, we provide a detailed description of the photoconversion technique and its applicability to tracking highly proliferating T cells from the priming site of T cell activation to peripheral target organs of effector function in a preclinical model. Dendra2+ T cells were photoconverted in the Peyer's patches during the initiation phase of acute graft-versus-host disease (GvHD) and tracked through the mesenteric lymph nodes and the peripheral blood to the small intestine with flow cytometry and intravital two-photon microscopy. Photoconverted alloreactive T cells preserved the full proliferative capacity, homing, and migration of alloreactive T cells in the intestinal lamina propria. We conclusively proved that photoconversion of highly proliferative alloreactive T cells in the Peyer's patches is an effective tool to study trafficking of alloreactive T cells under physiologic conditions and to GvHD target tissues. This technique can also be applied to the study of immune cell tracking under inflammatory and non-inflammatory conditions.},
  language  = {en}
}